Commit 9ab224ae3f8c20b3695861b8ee2095308b5a31d8 - tigr-glimmer

[svn-inject] Applying Debian modifications to trunk Charles Plessy 16 years ago

32 changed file(s) with 2917 addition(s) and 24 deletion(s). Raw diff Collapse all Expand all

+366

-17

Makefile less more

8	8	CFLAGS = -O3 -g -Wall
9	9	LDFLAGS = -lm
10	10
	11
	12	BINARIES = tigr-adjust tigr-anomaly tigr-build-icm tigr-check tigr-codon-usage tigr-compare-lists tigr-extract tigr-generate tigr-get-len tigr-get-putative tigr-glimmer2 tigr-long-orfs
11	13	DEPEND_FILES = .cc .c *.h
12		CLEANABLE_FILES = .o ~
13
14		ALL = adjust anomaly build-icm check codon-usage compare-lists \
15		extract generate get-len get-putative glimmer2 long-orfs
	14	CLEANABLE_FILES = .o ~ $(BINARIES)
	15	CLEANABLE_FILES += debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1
	16
	17	ALL = tigr-adjust tigr-anomaly tigr-build-icm tigr-check tigr-codon-usage tigr-compare-lists \
	18	tigr-extract tigr-generate tigr-get-len tigr-get-putative tigr-glimmer2 tigr-long-orfs
16	19
17	20	.SUFFIXES: .cc .c
18	21

24	27
25	28	all: $(ALL)
26	29
27		adjust: adjust.o delcher.o
	30	tigr-adjust: adjust.o delcher.o
28	31	$(CPPC) -o $(BINDIR)/$@ adjust.o delcher.o $(LDFLAGS)
29	32
30		anomaly: anomaly.o delcher.o gene.o
	33	tigr-anomaly: anomaly.o delcher.o gene.o
31	34	$(CPPC) -o $(BINDIR)/$@ anomaly.o delcher.o gene.o $(LDFLAGS)
32	35
33		build-icm: build-icm.o misc.o
	36	tigr-build-icm: build-icm.o misc.o
34	37	$(CC) -o $(BINDIR)/$@ build-icm.o misc.o $(LDFLAGS)
35	38
36		check: check.o delcher.o
	39	tigr-check: check.o delcher.o
37	40	$(CPPC) -o $(BINDIR)/$@ check.o delcher.o $(LDFLAGS)
38	41
39		codon-usage: codon-usage.o delcher.o gene.o
	42	tigr-codon-usage: codon-usage.o delcher.o gene.o
40	43	$(CPPC) -o $(BINDIR)/$@ codon-usage.o delcher.o gene.o $(LDFLAGS)
41	44
42		compare-lists: compare-lists.o delcher.o
	45	tigr-compare-lists: compare-lists.o delcher.o
43	46	$(CPPC) -o $(BINDIR)/$@ compare-lists.o delcher.o $(LDFLAGS)
44	47
45		extract: extract.o delcher.o
	48	tigr-extract: extract.o delcher.o
46	49	$(CPPC) -o $(BINDIR)/$@ extract.o delcher.o $(LDFLAGS)
47	50
48		generate: generate.o delcher.o gene.o
	51	tigr-generate: generate.o delcher.o gene.o
49	52	$(CPPC) -o $(BINDIR)/$@ generate.o delcher.o gene.o $(LDFLAGS)
50	53
51		get-len: get-len.o delcher.o
	54	tigr-get-len: get-len.o delcher.o
52	55	$(CPPC) -o $(BINDIR)/$@ get-len.o delcher.o $(LDFLAGS)
53	56
54		get-putative: get-putative.o delcher.o
	57	tigr-get-putative: get-putative.o delcher.o
55	58	$(CPPC) -o $(BINDIR)/$@ get-putative.o delcher.o $(LDFLAGS)
56	59
57		glimmer2: glimmer2.o delcher.o gene.o rnabin.o
	60	tigr-glimmer2: glimmer2.o delcher.o gene.o rnabin.o
58	61	$(CPPC) -o $(BINDIR)/$@ glimmer2.o delcher.o gene.o rnabin.o $(LDFLAGS)
59	62
60		long-orfs: long-orfs.o delcher.o gene.o
	63	tigr-long-orfs: long-orfs.o delcher.o gene.o
61	64	$(CPPC) -o $(BINDIR)/$@ long-orfs.o delcher.o gene.o $(LDFLAGS)
62	65
63		rnabin: rnabin.o delcher.o
	66	tigr-rnabin: rnabin.o delcher.o
64	67	$(CPPC) -o $(BINDIR)/$@ rnabin.o delcher.o $(LDFLAGS)
65	68
66	69	depend:

71	74
72	75	# DO NOT DELETE THIS LINE -- make depend depends on it.
73	76
	77	adjust.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	78	adjust.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	79	adjust.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	80	adjust.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	81	adjust.o: /usr/include/_G_config.h /usr/include/wchar.h
	82	adjust.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	83	adjust.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	84	adjust.o: /usr/include/stdlib.h /usr/include/math.h
	85	adjust.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	86	adjust.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	87	adjust.o: /usr/include/ctype.h /usr/include/endian.h
	88	adjust.o: /usr/include/bits/endian.h /usr/include/limits.h
	89	adjust.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	90	adjust.o: /usr/include/errno.h /usr/include/bits/errno.h
	91	adjust.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	92	adjust.o: /usr/include/asm-generic/errno.h
	93	adjust.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	94	adjust.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	95	anomaly.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	96	anomaly.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	97	anomaly.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	98	anomaly.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	99	anomaly.o: /usr/include/_G_config.h /usr/include/wchar.h
	100	anomaly.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	101	anomaly.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	102	anomaly.o: /usr/include/stdlib.h /usr/include/math.h
	103	anomaly.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	104	anomaly.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	105	anomaly.o: /usr/include/ctype.h /usr/include/endian.h
	106	anomaly.o: /usr/include/bits/endian.h /usr/include/limits.h
	107	anomaly.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	108	anomaly.o: /usr/include/errno.h /usr/include/bits/errno.h
	109	anomaly.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	110	anomaly.o: /usr/include/asm-generic/errno.h
	111	anomaly.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	112	anomaly.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
	113	check.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	114	check.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	115	check.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	116	check.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	117	check.o: /usr/include/_G_config.h /usr/include/wchar.h
	118	check.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	119	check.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	120	check.o: /usr/include/stdlib.h /usr/include/math.h
	121	check.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	122	check.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	123	check.o: /usr/include/ctype.h /usr/include/endian.h
	124	check.o: /usr/include/bits/endian.h /usr/include/limits.h /usr/include/time.h
	125	check.o: /usr/include/bits/time.h /usr/include/assert.h /usr/include/errno.h
	126	check.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	127	check.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	128	check.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	129	check.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	130	codon-usage.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	131	codon-usage.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	132	codon-usage.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	133	codon-usage.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	134	codon-usage.o: /usr/include/_G_config.h /usr/include/wchar.h
	135	codon-usage.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	136	codon-usage.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	137	codon-usage.o: /usr/include/stdlib.h /usr/include/math.h
	138	codon-usage.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	139	codon-usage.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	140	codon-usage.o: /usr/include/ctype.h /usr/include/endian.h
	141	codon-usage.o: /usr/include/bits/endian.h /usr/include/limits.h
	142	codon-usage.o: /usr/include/time.h /usr/include/bits/time.h
	143	codon-usage.o: /usr/include/assert.h /usr/include/errno.h
	144	codon-usage.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	145	codon-usage.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	146	codon-usage.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	147	codon-usage.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	148	codon-usage.o: gene.h
	149	compare-lists.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	150	compare-lists.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	151	compare-lists.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	152	compare-lists.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	153	compare-lists.o: /usr/include/_G_config.h /usr/include/wchar.h
	154	compare-lists.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	155	compare-lists.o: /usr/include/bits/stdio_lim.h
	156	compare-lists.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h
	157	compare-lists.o: /usr/include/math.h /usr/include/bits/huge_val.h
	158	compare-lists.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
	159	compare-lists.o: /usr/include/string.h /usr/include/ctype.h
	160	compare-lists.o: /usr/include/endian.h /usr/include/bits/endian.h
	161	compare-lists.o: /usr/include/limits.h /usr/include/time.h
	162	compare-lists.o: /usr/include/bits/time.h /usr/include/assert.h
	163	compare-lists.o: /usr/include/errno.h /usr/include/bits/errno.h
	164	compare-lists.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	165	compare-lists.o: /usr/include/asm-generic/errno.h
	166	compare-lists.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	167	compare-lists.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	168	delcher.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	169	delcher.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	170	delcher.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	171	delcher.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	172	delcher.o: /usr/include/_G_config.h /usr/include/wchar.h
	173	delcher.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	174	delcher.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	175	delcher.o: /usr/include/stdlib.h /usr/include/math.h
	176	delcher.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	177	delcher.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	178	delcher.o: /usr/include/ctype.h /usr/include/endian.h
	179	delcher.o: /usr/include/bits/endian.h /usr/include/limits.h
	180	delcher.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	181	delcher.o: /usr/include/errno.h /usr/include/bits/errno.h
	182	delcher.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	183	delcher.o: /usr/include/asm-generic/errno.h
	184	delcher.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	185	delcher.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	186	extract.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	187	extract.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	188	extract.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	189	extract.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	190	extract.o: /usr/include/_G_config.h /usr/include/wchar.h
	191	extract.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	192	extract.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	193	extract.o: /usr/include/stdlib.h /usr/include/math.h
	194	extract.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	195	extract.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	196	extract.o: /usr/include/ctype.h /usr/include/endian.h
	197	extract.o: /usr/include/bits/endian.h /usr/include/limits.h
	198	extract.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	199	extract.o: /usr/include/errno.h /usr/include/bits/errno.h
	200	extract.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	201	extract.o: /usr/include/asm-generic/errno.h
	202	extract.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	203	extract.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	204	gene.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	205	gene.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	206	gene.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	207	gene.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	208	gene.o: /usr/include/_G_config.h /usr/include/wchar.h
	209	gene.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	210	gene.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	211	gene.o: /usr/include/stdlib.h /usr/include/math.h
	212	gene.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	213	gene.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	214	gene.o: /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h
	215	gene.o: /usr/include/limits.h /usr/include/time.h /usr/include/bits/time.h
	216	gene.o: /usr/include/assert.h /usr/include/errno.h /usr/include/bits/errno.h
	217	gene.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	218	gene.o: /usr/include/asm-generic/errno.h
	219	gene.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	220	gene.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
	221	generate.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	222	generate.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	223	generate.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	224	generate.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	225	generate.o: /usr/include/_G_config.h /usr/include/wchar.h
	226	generate.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	227	generate.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	228	generate.o: /usr/include/stdlib.h /usr/include/math.h
	229	generate.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	230	generate.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	231	generate.o: /usr/include/ctype.h /usr/include/endian.h
	232	generate.o: /usr/include/bits/endian.h /usr/include/limits.h
	233	generate.o: /usr/include/time.h /usr/include/bits/time.h
	234	generate.o: /usr/include/assert.h /usr/include/errno.h
	235	generate.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	236	generate.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	237	generate.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	238	generate.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
	239	generate.o: icm.h
	240	get-len.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	241	get-len.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	242	get-len.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	243	get-len.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	244	get-len.o: /usr/include/_G_config.h /usr/include/wchar.h
	245	get-len.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	246	get-len.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	247	get-len.o: /usr/include/stdlib.h /usr/include/math.h
	248	get-len.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	249	get-len.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	250	get-len.o: /usr/include/ctype.h /usr/include/endian.h
	251	get-len.o: /usr/include/bits/endian.h /usr/include/limits.h
	252	get-len.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	253	get-len.o: /usr/include/errno.h /usr/include/bits/errno.h
	254	get-len.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	255	get-len.o: /usr/include/asm-generic/errno.h
	256	get-len.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	257	get-len.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	258	get-putative.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	259	get-putative.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	260	get-putative.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	261	get-putative.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	262	get-putative.o: /usr/include/_G_config.h /usr/include/wchar.h
	263	get-putative.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	264	get-putative.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	265	get-putative.o: /usr/include/stdlib.h /usr/include/math.h
	266	get-putative.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	267	get-putative.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	268	get-putative.o: /usr/include/ctype.h /usr/include/endian.h
	269	get-putative.o: /usr/include/bits/endian.h /usr/include/limits.h
	270	get-putative.o: /usr/include/time.h /usr/include/bits/time.h
	271	get-putative.o: /usr/include/assert.h /usr/include/errno.h
	272	get-putative.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	273	get-putative.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	274	get-putative.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	275	get-putative.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	276	glimmer2.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	277	glimmer2.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	278	glimmer2.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	279	glimmer2.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	280	glimmer2.o: /usr/include/_G_config.h /usr/include/wchar.h
	281	glimmer2.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	282	glimmer2.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	283	glimmer2.o: /usr/include/stdlib.h /usr/include/math.h
	284	glimmer2.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	285	glimmer2.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	286	glimmer2.o: /usr/include/ctype.h /usr/include/endian.h
	287	glimmer2.o: /usr/include/bits/endian.h /usr/include/limits.h
	288	glimmer2.o: /usr/include/time.h /usr/include/bits/time.h
	289	glimmer2.o: /usr/include/assert.h /usr/include/errno.h
	290	glimmer2.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	291	glimmer2.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	292	glimmer2.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	293	glimmer2.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
	294	glimmer2.o: icm.h
	295	long-orfs.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	296	long-orfs.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	297	long-orfs.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	298	long-orfs.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	299	long-orfs.o: /usr/include/_G_config.h /usr/include/wchar.h
	300	long-orfs.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	301	long-orfs.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	302	long-orfs.o: /usr/include/stdlib.h /usr/include/math.h
	303	long-orfs.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	304	long-orfs.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	305	long-orfs.o: /usr/include/ctype.h /usr/include/endian.h
	306	long-orfs.o: /usr/include/bits/endian.h /usr/include/limits.h
	307	long-orfs.o: /usr/include/time.h /usr/include/bits/time.h
	308	long-orfs.o: /usr/include/assert.h /usr/include/errno.h
	309	long-orfs.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	310	long-orfs.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	311	long-orfs.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	312	long-orfs.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	313	long-orfs.o: gene.h
	314	rnabin.o: rnabin.h delcher.h /usr/include/stdio.h /usr/include/features.h
	315	rnabin.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	316	rnabin.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	317	rnabin.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	318	rnabin.o: /usr/include/_G_config.h /usr/include/wchar.h
	319	rnabin.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	320	rnabin.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	321	rnabin.o: /usr/include/stdlib.h /usr/include/math.h
	322	rnabin.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	323	rnabin.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	324	rnabin.o: /usr/include/ctype.h /usr/include/endian.h
	325	rnabin.o: /usr/include/bits/endian.h /usr/include/limits.h
	326	rnabin.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	327	rnabin.o: /usr/include/errno.h /usr/include/bits/errno.h
	328	rnabin.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	329	rnabin.o: /usr/include/asm-generic/errno.h
	330	rnabin.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	331	rnabin.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h
	332	translate.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	333	translate.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	334	translate.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	335	translate.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	336	translate.o: /usr/include/_G_config.h /usr/include/wchar.h
	337	translate.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	338	translate.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	339	translate.o: /usr/include/stdlib.h /usr/include/math.h
	340	translate.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	341	translate.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	342	translate.o: /usr/include/ctype.h /usr/include/endian.h
	343	translate.o: /usr/include/bits/endian.h /usr/include/limits.h
	344	translate.o: /usr/include/time.h /usr/include/bits/time.h
	345	translate.o: /usr/include/assert.h /usr/include/errno.h
	346	translate.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	347	translate.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	348	translate.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	349	translate.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	350	build-icm.o: /usr/include/stdlib.h /usr/include/features.h
	351	build-icm.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	352	build-icm.o: /usr/include/stdio.h /usr/include/bits/types.h
	353	build-icm.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
	354	build-icm.o: /usr/include/libio.h /usr/include/_G_config.h
	355	build-icm.o: /usr/include/wchar.h /usr/include/bits/wchar.h
	356	build-icm.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h
	357	build-icm.o: /usr/include/bits/sys_errlist.h /usr/include/math.h
	358	build-icm.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	359	build-icm.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	360	build-icm.o: /usr/include/ctype.h /usr/include/endian.h
	361	build-icm.o: /usr/include/bits/endian.h /usr/include/unistd.h
	362	build-icm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	363	build-icm.o: build-icm.h misc.h
	364	misc.o: /usr/include/stdlib.h /usr/include/features.h
	365	misc.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	366	misc.o: /usr/include/stdio.h /usr/include/bits/types.h
	367	misc.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
	368	misc.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
	369	misc.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	370	misc.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h misc.h
	371	delcher.o: /usr/include/stdio.h /usr/include/features.h
	372	delcher.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	373	delcher.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	374	delcher.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	375	delcher.o: /usr/include/_G_config.h /usr/include/wchar.h
	376	delcher.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	377	delcher.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	378	delcher.o: /usr/include/stdlib.h /usr/include/math.h
	379	delcher.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	380	delcher.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	381	delcher.o: /usr/include/ctype.h /usr/include/endian.h
	382	delcher.o: /usr/include/bits/endian.h /usr/include/limits.h
	383	delcher.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	384	delcher.o: /usr/include/errno.h /usr/include/bits/errno.h
	385	delcher.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	386	delcher.o: /usr/include/asm-generic/errno.h
	387	delcher.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	388	delcher.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	389	icm.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	390	icm.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	391	icm.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	392	icm.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	393	icm.o: /usr/include/_G_config.h /usr/include/wchar.h
	394	icm.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	395	icm.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	396	icm.o: /usr/include/stdlib.h /usr/include/math.h /usr/include/bits/huge_val.h
	397	icm.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
	398	icm.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
	399	icm.o: /usr/include/bits/endian.h /usr/include/limits.h /usr/include/time.h
	400	icm.o: /usr/include/bits/time.h /usr/include/assert.h /usr/include/errno.h
	401	icm.o: /usr/include/bits/errno.h /usr/include/linux/errno.h
	402	icm.o: /usr/include/asm/errno.h /usr/include/asm-generic/errno.h
	403	icm.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	404	icm.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
	405	rnabin.o: delcher.h /usr/include/stdio.h /usr/include/features.h
	406	rnabin.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
	407	rnabin.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
	408	rnabin.o: /usr/include/bits/typesizes.h /usr/include/libio.h
	409	rnabin.o: /usr/include/_G_config.h /usr/include/wchar.h
	410	rnabin.o: /usr/include/bits/wchar.h /usr/include/gconv.h
	411	rnabin.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
	412	rnabin.o: /usr/include/stdlib.h /usr/include/math.h
	413	rnabin.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
	414	rnabin.o: /usr/include/bits/mathcalls.h /usr/include/string.h
	415	rnabin.o: /usr/include/ctype.h /usr/include/endian.h
	416	rnabin.o: /usr/include/bits/endian.h /usr/include/limits.h
	417	rnabin.o: /usr/include/time.h /usr/include/bits/time.h /usr/include/assert.h
	418	rnabin.o: /usr/include/errno.h /usr/include/bits/errno.h
	419	rnabin.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
	420	rnabin.o: /usr/include/asm-generic/errno.h
	421	rnabin.o: /usr/include/asm-generic/errno-base.h /usr/include/unistd.h
	422	rnabin.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h gene.h

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debian/NEWS.Debian less more

	0	With version 2.13-1, the binaries and man pages all have a prefix "tigr-"
	1	to avoid conflicts with other programs, with extract in particular.
	2
	3	-- Steffen Moeller <moeller@pzr.uni-rostock.de>, Thu, 10 Nov 2004 17:33:46 +0100
	4

+15

-0

debian/README.Debian less more

	0	tigr-glimmer for Debian
	1	-----------------------
	2
	3	The glimmer software of the TIGR institute was renamed to tigr-glimmer
	4	because of a name conflict with the GNOME library. The package works
	5	for me, most efforts went into the reformatting of the readme files
	6	for the man pages, feedback is welcome.
	7
	8	The upstream authors are very supportive of this debian package for
	9	their software and I thank them for this.
	10
	11	With version 2.13-1, the binaries and man pages all have a prefix "tigr-"
	12	to avoid conflicts with other programs, with extract in particular.
	13
	14	-- Steffen Moeller <moeller@pzr.uni-rostock.de>, Thu, 10 Nov 2004 12:33:46 +0100

+21

-0

debian/changelog less more

	0	tigr-glimmer (2.13-1.1) unstable; urgency=low
	1
	2	* Non-maintainer upload.
	3	* Fix GCC 4.3 compatibility, patch by Kumar Appaiah (Closes: #461691)
	4
	5	-- Moritz Muehlenhoff <jmm@debian.org> Thu, 20 Mar 2008 00:02:06 +0100
	6
	7	tigr-glimmer (2.13-1) unstable; urgency=low
	8
	9	* New upstream release - no significant changes for Linux users.
	10	* Resolves conflict for "extract" binary and man page (Closes:Bug#227790,Bug#274780).
	11
	12	-- Steffen Moeller <moeller@pzr.uni-rostock.de> Wed, 10 Nov 2004 11:58:46 +0100
	13
	14	tigr-glimmer (2.12-1) unstable; urgency=low
	15
	16	* Initial Release (Closes:#219453).
	17	* Added man pages to upstream release
	18
	19	-- Steffen Moeller <moeller@pzr.uni-rostock.de> Thu, 16 Oct 2003 17:33:46 +0200
	20

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debian/compat less more

+20

-0

debian/control less more

	0	Source: tigr-glimmer
	1	Section: science
	2	Priority: optional
	3	Maintainer: Steffen Moeller <moeller@pzr.uni-rostock.de>
	4	Build-Depends: debhelper (>= 4.0.0), docbook-to-man, gzip, cdbs
	5	Standards-Version: 3.6.0
	6
	7	Package: tigr-glimmer
	8	Architecture: any
	9	Depends: ${shlibs:Depends}, ${misc:Depends}
	10	Description: [Biology] Gene detection in archea and bacteria
	11	Developed by the TIGR institute this software detects coding sequences in
	12	bacteria and archea.
	13	.
	14	Glimmer is a system for finding genes in microbial DNA, especially the
	15	genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated
	16	Markov Modeler) uses interpolated Markov models (IMMs) to identify the
	17	coding regions and distinguish them from noncoding DNA.
	18	.
	19	Homepage: http://www.tigr.org/software/glimmer/

+137

-0

debian/copyright less more

	0	This package was debianized by Steffen Moeller <moeller@pzr.uni-rostock.de> on
	1	Thu, 16 Oct 2003 17:33:46 +0200.
	2
	3	It was downloaded from ftp://ftp.tigr.org/software/glimmer/
	4
	5	Upstream Authors:
	6	Art Delcher <adelcher@tigr.org>
	7	Steven Salzberg <salzberg@tigr.org>
	8
	9	Copyright:
	10
	11	-=- Glimmer 2.1x COPYRIGHT NOTICE -=-
	12
	13	Copyright (c) 1998-2003 by The Institute for Genomic
	14	Research (TIGR), Rockville, Maryland, U.S.A. All rights reserved.
	15
	16	This software is OSI Certified Open Source Software. OSI Certified is a
	17	certification mark of the Open Source Initiative. Please refer to the
	18	'LICENSE' file for more information and the 'ACKNOWLEDGEMENTS' file for
	19	names of contributors to the code base.
	20
	21	-=- GLIMMER 2.1x OPEN SOURCE LICENSE -=-
	22
	23	The Artistic License
	24
	25	Preamble
	26
	27	The intent of this document is to state the conditions under which a
	28	Package may be copied, such that the Copyright Holder maintains some
	29	semblance of artistic control over the development of the package,
	30	while giving the users of the package the right to use and distribute
	31	the Package in a more-or-less customary fashion, plus the right to
	32	make reasonable modifications.
	33
	34	Definitions:
	35	* "Package" refers to the collection of files distributed by the
	36	Copyright Holder, and derivatives of that collection of files
	37	created through textual modification.
	38	* "Standard Version" refers to such a Package if it has not been
	39	modified, or has been modified in accordance with the wishes of
	40	the Copyright Holder.
	41	* "Copyright Holder" is whoever is named in the copyright or
	42	copyrights for the package.
	43	* "You" is you, if you're thinking about copying or distributing
	44	this Package.
	45	* "Reasonable copying fee" is whatever you can justify on the
	46	basis of media cost, duplication charges, time of people
	47	involved, and so on. (You will not be required to justify it to
	48	the Copyright Holder, but only to the computing community at
	49	large as a market that must bear the fee.)
	50	* "Freely Available" means that no fee is charged for the item
	51	itself, though there may be fees involved in handling the
	52	item. It also means that recipients of the item may redistribute
	53	it under the same conditions they received it.
	54
	55	1. You may make and give away verbatim copies of the source form of
	56	the Standard Version of this Package without restriction, provided
	57	that you duplicate all of the original copyright notices and
	58	associated disclaimers.
	59
	60	2. You may apply bug fixes, portability fixes and other modifications
	61	derived from the Public Domain or from the Copyright Holder. A
	62	Package modified in such a way shall still be considered the
	63	Standard Version.
	64
	65	3. You may otherwise modify your copy of this Package in any way,
	66	provided that you insert a prominent notice in each changed file
	67	stating how and when you changed that file, and provided that you
	68	do at least ONE of the following:
	69
	70	a) place your modifications in the Public Domain or otherwise make
	71	them Freely Available, such as by posting said modifications to
	72	Usenet or an equivalent medium, or placing the modifications on a
	73	major archive site such as ftp.uu.net, or by allowing the
	74	Copyright Holder to include your modifications in the Standard
	75	Version of the Package.
	76
	77	b) use the modified Package only within your corporation or
	78	organization.
	79
	80	c) rename any non-standard executables so the names do not
	81	conflict with standard executables, which must also be provided,
	82	and provide a separate manual page for each non-standard
	83	executable that clearly documents how it differs from the Standard
	84	Version.
	85
	86	d) make other distribution arrangements with the Copyright Holder.
	87
	88	4. You may distribute the programs of this Package in object code or
	89	executable form, provided that you do at least ONE of the
	90	following:
	91
	92	a) distribute a Standard Version of the executables and library
	93	files, together with instructions (in the manual page or
	94	equivalent) on where to get the Standard Version.
	95
	96	b) accompany the distribution with the machine-readable source of
	97	the Package with your modifications.
	98
	99	c) accompany any non-standard executables with their corresponding
	100	Standard Version executables, giving the non-standard executables
	101	non-standard names, and clearly documenting the differences in
	102	manual pages (or equivalent), together with instructions on where
	103	to get the Standard Version.
	104
	105	d) make other distribution arrangements with the Copyright Holder.
	106
	107	5. You may charge a reasonable copying fee for any distribution of
	108	this Package. You may charge any fee you choose for support of this
	109	Package. You may not charge a fee for this Package itself. However,
	110	you may distribute this Package in aggregate with other (possibly
	111	commercial) programs as part of a larger (possibly commercial)
	112	software distribution provided that you do not advertise this
	113	Package as a product of your own.
	114
	115	6. The scripts and library files supplied as input to or produced as
	116	output from the programs of this Package do not automatically fall
	117	under the copyright of this Package, but belong to whomever
	118	generated them, and may be sold commercially, and may be aggregated
	119	with this Package.
	120
	121	7. C or perl subroutines supplied by you and linked into this Package
	122	shall not be considered part of this Package.
	123
	124	8. The name of the Copyright Holder may not be used to endorse or
	125	promote products derived from this software without specific prior
	126	written permission.
	127
	128	9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
	129	WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
	130	OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
	131
	132	The End
	133	This license is approved by the Open Source Initiative
	134	(www.opensource.org) for certifying software as OSI Certified Open
	135	Source.
	136

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debian/dirs less more

usr/bin

-0

debian/docs less more

	0	README
	1	ACKNOWLEDGEMENTS
	2	changelog.gz
	3	build-icm.readme
	4	extract.readme
	5	glimmer2.readme
	6	long-orfs.readme

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debian/glimmer.substvars less more

shlibs:Depends=libc6 (>= 2.3.2-1), libgcc1 (>= 1:3.3.1-1), libstdc++5 (>= 1:3.3.1-1)

+168

-0

debian/index.html less more

	0	<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
	1	<HTML
	2	><HEAD
	3	><TITLE
	4	>EXTRACT</TITLE
	5	><META
	6	NAME="GENERATOR"
	7	CONTENT="Modular DocBook HTML Stylesheet Version 1.7"></HEAD
	8	><BODY
	9	CLASS="REFENTRY"
	10	BGCOLOR="#FFFFFF"
	11	TEXT="#000000"
	12	LINK="#0000FF"
	13	VLINK="#840084"
	14	ALINK="#0000FF"
	15	><H1
	16	><A
	17	NAME="AEN1"
	18	></A
	19	>EXTRACT</H1
	20	><DIV
	21	CLASS="REFNAMEDIV"
	22	><A
	23	NAME="AEN15"
	24	></A
	25	><H2
	26	>Name</H2
	27	>extract -- Fine start/stop positions of genes in genome sequence</DIV
	28	><DIV
	29	CLASS="REFSYNOPSISDIV"
	30	><A
	31	NAME="AEN18"
	32	></A
	33	><H2
	34	>Synopsis</H2
	35	><P
	36	><B
	37	CLASS="COMMAND"
	38	>long-orgs</B
	39	> [genome-file <VAR
	40	CLASS="OPTION"
	41	><VAR
	42	CLASS="REPLACEABLE"
	43	>options</VAR
	44	></VAR
	45	>]</P
	46	></DIV
	47	><DIV
	48	CLASS="REFSECT1"
	49	><A
	50	NAME="AEN24"
	51	></A
	52	><H2
	53	>DESCRIPTION</H2
	54	><P
	55	>Program extract takes a FASTA format sequence file and a file
	56	with a list of start/stop positions in that file (e.g., as produced
	57	by the long-orfs program) and extracts and outputs the
	58	specified sequences.</P
	59	><P
	60	>The first command-line argument is the name of the sequence file,
	61	which must be in FASTA format.</P
	62	><P
	63	>The second command-line argument is the name of the coordinate file.
	64	It must contain a list of pairs of positions in the first file, one
	65	per line. The format of each entry is:</P
	66	><P
	67	> <IDstring>> <start position> <stop position></P
	68	><P
	69	>This file should contain no other information, so if you're using
	70	the output of glimmer or long-orfs , you'll have to cut off
	71	header lines.</P
	72	><P
	73	>The output of the program goes to the standard output and has one
	74	line for each line in the coordinate file. Each line contains
	75	the IDstring , followed by white space, followed by the substring
	76	of the sequence file specified by the coordinate pair. Specifically,
	77	the substring starts at the first position of the pair and ends at
	78	the second position (inclusive). If the first position is bigger
	79	than the second, then the DNA reverse complement of each position
	80	is generated. Start/stop pairs that "wrap around" the end of the
	81	genome are allowed.</P
	82	></DIV
	83	><DIV
	84	CLASS="REFSECT1"
	85	><A
	86	NAME="AEN32"
	87	></A
	88	><H2
	89	>OPTIONS</H2
	90	><P
	91	></P
	92	><DIV
	93	CLASS="VARIABLELIST"
	94	><DL
	95	><DT
	96	><VAR
	97	CLASS="OPTION"
	98	>-skip</VAR
	99	></DT
	100	><DD
	101	><P
	102	> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</P
	103	></DD
	104	><DT
	105	><VAR
	106	CLASS="OPTION"
	107	>-l</VAR
	108	></DT
	109	><DD
	110	><P
	111	> makes the output omit an sequences shorter than n characters.
	112	n includes the 3 skipped characters if the -skip switch
	113	is one.
	114	</P
	115	></DD
	116	></DL
	117	></DIV
	118	></DIV
	119	><DIV
	120	CLASS="REFSECT1"
	121	><A
	122	NAME="AEN45"
	123	></A
	124	><H2
	125	>SEE ALSO</H2
	126	><P
	127	>glimmer2 (1),
	128	long-orfs (1),
	129	adjust (1),
	130	anomaly (1),
	131	build-icm (1),
	132	check (1),
	133	codon-usage (1),
	134	compare-lists (1),
	135	extract (1),
	136	generate (1),
	137	get-len (1),
	138	get-putative (1),</P
	139	><P
	140	>http://www.tigr.org/software/glimmer/</P
	141	><P
	142	>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</P
	143	></DIV
	144	><DIV
	145	CLASS="REFSECT1"
	146	><A
	147	NAME="AEN50"
	148	></A
	149	><H2
	150	>AUTHOR</H2
	151	><P
	152	>This manual page was quickly copied from the glimmer web site by Steffen Moeller <CODE
	153	CLASS="EMAIL"
	154	><<A
	155	HREF="mailto:moeller@pzr.uni-rostock.de"
	156	>moeller@pzr.uni-rostock.de</A
	157	>></CODE
	158	> for
	159	the <SPAN
	160	CLASS="PRODUCTNAME"
	161	>Debian</SPAN
	162	> system.
	163	</P
	164	></DIV
	165	></BODY
	166	></HTML
	167	>⏎

+13

-0

debian/install less more

	0	tigr-adjust usr/bin
	1	tigr-anomaly usr/bin
	2	tigr-build-icm usr/bin
	3	tigr-check usr/bin
	4	tigr-codon-usage usr/bin
	5	tigr-compare-lists usr/bin
	6	tigr-extract usr/bin
	7	tigr-generate usr/bin
	8	tigr-get-len usr/bin
	9	tigr-get-putative usr/bin
	10	tigr-glimmer2 usr/bin
	11	tigr-long-orfs usr/bin
	12	tigr-run-glimmer2 usr/bin

+190

-0

debian/long-orfs.1 less more

	0	...\" $Header: /aolnet/dev/src/CVS/sgml/docbook-to-man/cmd/docbook-to-man.sh,v 1.1.1.1 1998/11/13 21:31:59 db3l Exp $
	1	...\"
	2	...\" transcript compatibility for postscript use.
	3	...\"
	4	...\" synopsis: .P! <file.ps>
	5	...\"
	6	.de P!
	7	.fl
	8	\!!1 setgray
	9	.fl
	10	\\&.\"
	11	.fl
	12	\!!0 setgray
	13	.fl \" force out current output buffer
	14	\!!save /psv exch def currentpoint translate 0 0 moveto
	15	\!!/showpage{}def
	16	.fl \" prolog
	17	.sy sed -e 's/^/!/' \\$1\" bring in postscript file
	18	\!!psv restore
	19	.
	20	.de pF
	21	.ie \\*(f1 .ds f1 \\n(.f
	22	.el .ie \\*(f2 .ds f2 \\n(.f
	23	.el .ie \\*(f3 .ds f3 \\n(.f
	24	.el .ie \\*(f4 .ds f4 \\n(.f
	25	.el .tm ? font overflow
	26	.ft \\$1
	27	..
	28	.de fP
	29	.ie !\\*(f4 \{\
	30	. ft \\*(f4
	31	. ds f4\"
	32	' br \}
	33	.el .ie !\\*(f3 \{\
	34	. ft \\*(f3
	35	. ds f3\"
	36	' br \}
	37	.el .ie !\\*(f2 \{\
	38	. ft \\*(f2
	39	. ds f2\"
	40	' br \}
	41	.el .ie !\\*(f1 \{\
	42	. ft \\*(f1
	43	. ds f1\"
	44	' br \}
	45	.el .tm ? font underflow
	46	..
	47	.ds f1\"
	48	.ds f2\"
	49	.ds f3\"
	50	.ds f4\"
	51	'\" t
	52	.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n
	53	.TH "LONG-ORFS" "1"
	54	.SH "NAME"
	55	long-orfs \(em Find/Score potential genes in genome-file using
	56	the probability model in icm-file
	57	.SH "SYNOPSIS"
	58	.PP
	59	\fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP]
	60	.SH "DESCRIPTION"
	61	.PP
	62	Program long-orfs takes a sequence file (in FASTA format) and
	63	outputs a list of all long "potential genes" in it that do not
	64	overlap by too much. By "potential gene" I mean the portion of
	65	an orf from the first start codon to the stop codon at the end.
	66	.PP
	67	The first few lines of output specify the settings of various
	68	parameters in the program:
	69	.PP
	70	Minimum gene length is the length of the smallest fragment
	71	considered to be a gene. The length is measured from the first base
	72	of the start codon to the last base before the stop codon.
	73	This value can be specified when running the program with the -g option.
	74	By default, the program now (April 2003) will compute an optimal length
	75	for this parameter, where "optimal" is the value that produces the
	76	greatest number of long ORFs, thereby increasing the amount of data
	77	used for training.
	78	.PP
	79	Minimum overlap length is a lower bound on the number of bases overlap
	80	between 2 genes that is considered a problem. Overlaps shorter than
	81	this are ignored.
	82	.PP
	83	Minimum overlap percent is another lower bound on the number of bases
	84	overlap that is considered a problem. Overlaps shorter than this
	85	percentage of both genes are ignored.
	86	.PP
	87	The next portion of the output is a list of potential genes:
	88	.PP
	89	Column 1 is an ID number for reference purposes. It is assigned
	90	sequentially starting with 1 to all long potential genes. If
	91	overlapping genes are eliminated, gaps in the numbers will occur.
	92	The ID prefix is specified in the constant ID_PREFIX .
	93	.PP
	94	Column 2 is the position of the first base of the first start codon in
	95	the orf. Currently I use atg, and gtg as start codons. This is
	96	easily changed in the function Is_Start () .
	97	.PP
	98	Column 3 is the position of the last base before the stop codon. Stop
	99	codons are taa, tag, and tga. Note that for orfs in the reverse
	100	reading frames have their start position higher than the end position.
	101	The order in which orfs are listed is in increasing order by
	102	Max {OrfStart, End}, i.e., the highest numbered position in the orf,
	103	except for orfs that "wrap around" the end of the sequence.
	104	.PP
	105	When two genes with ID numbers overlap by at least a sufficient
	106	amount (as determined by Min_Olap and Min_Olap_Percent ), they
	107	are eliminated and do not appear in the output.
	108	.PP
	109	The final output of the program (sent to the standard error file so
	110	it does not show up when output is redirected to a file) is the
	111	length of the longest orf found.
	112	.PP
	113
	114	Specifying Different Start and Stop Codons:
	115	.PP
	116	To specify different sets of start and stop codons, modify the file
	117	gene.h . Specifically, the functions:
	118	.PP
	119	Is_Forward_Start Is_Reverse_Start Is_Start
	120	Is_Forward_Stop Is_Reverse_Stop Is_Stop
	121	.PP
	122	are used to determine what is used for start and stop codons.
	123	.PP
	124	Is_Start and Is_Stop do simple string comparisons to specify
	125	which patterns are used. To add a new pattern, just add the comparison
	126	for it. To remove a pattern, comment out or delete the comparison
	127	for it.
	128	.PP
	129	The other four functions use a bit comparison to determine start and
	130	stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
	131	for each base, one bit for each possible value of the bases, T, G, C
	132	or A. Thus the bit pattern 0010 0101 1100 represents the base
	133	pattern [C] [A or G] [G or T]. By doing bit operations (& \| ~) and
	134	comparisons, more complicated patterns involving ambiguous reads
	135	can be tested efficiently. Simple patterns can be tested as in
	136	the current code.
	137	.PP
	138	For example, to insert an additional start codon of CAT requires 3 changes:
	139	1. The line
	140	\|\| (Codon & 0x218) == Codon
	141	should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
	142	represents CAT.
	143	2. The line
	144	\|\| (Codon & 0x184) == Codon
	145	should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
	146	represents ATG, which is the reverse-complement of CAT. Alternately,
	147	the #define constant ATG_MASK could be used.
	148	3. The line
	149	\|\| strncmp (S, "cat", 3) == 0
	150	should be inserted into Is_Start .
	151	.SH "OPTIONS"
	152	.IP "\fB-g \fIn\fR\fP" 10
	153	Set minimum gene length to n. Default is to compute an
	154	optimal value automatically. Don't change this unless you
	155	know what you're doing.
	156	.IP "\fB-l\fP" 10
	157	Regard the genome as linear (not circular), i.e., do not allow
	158	genes to "wrap around" the end of the genome.
	159	This option works on both glimmer and long-orfs .
	160	The default behavior is to regard the genome as circular.
	161	.IP "\fB-o \fIn\fR\fP" 10
	162	Set maximum overlap length to n. Overlaps shorter than this
	163	are permitted. (Default is 0 bp.)
	164	.IP "\fB-p \fIn\fR\fP" 10
	165	Set maximum overlap percentage to n%. Overlaps shorter than
	166	this percentage of both strings are ignored. (Default is 10%.)
	167	.SH "SEE ALSO"
	168	.PP
	169	glimmer2 (1),
	170	adjust (1),
	171	anomaly (1),
	172	build-icm (1),
	173	check (1),
	174	codon-usage (1),
	175	compare-lists (1),
	176	extract (1),
	177	generate (1),
	178	get-len (1),
	179	get-putative (1),
	180	.PP
	181	http://www.tigr.org/software/glimmer/
	182	.PP
	183	Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.
	184	.SH "AUTHOR"
	185	.PP
	186	This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@pzr.uni-rostock.de for
	187	the \fBDebian\fP system.
	188
	189	...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43

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debian/manpages less more

	0	debian/tigr-adjust.1
	1	debian/tigr-anomaly.1
	2	debian/tigr-build-icm.1
	3	debian/tigr-check.1
	4	debian/tigr-codon-usage.1
	5	debian/tigr-compare-lists.1
	6	debian/tigr-extract.1
	7	debian/tigr-generate.1
	8	debian/tigr-get-len.1
	9	debian/tigr-get-putative.1
	10	debian/tigr-glimmer2.1
	11	debian/tigr-long-orfs.1
	12	debian/tigr-run-glimmer2.1

-0

debian/manpages.links less more

tigr-glimmer glimmer2

+58

-0

debian/rules less more

	0	#!/usr/bin/make -f
	1	# -- makefile --
	2	# Sample debian/rules that uses debhelper.
	3	# GNU copyright 1997 to 1999 by Joey Hess.
	4	#
	5	# Modified to make a template file for a multi-binary package with separated
	6	# build-arch and build-indep targets by Bill Allombert 2001
	7
	8	# Uncomment this to turn on verbose mode.
	9	#export DH_VERBOSE=1
	10
	11	.PHONY: clean
	12
	13	include /usr/share/cdbs/1/rules/debhelper.mk
	14	include /usr/share/cdbs/1/class/langcore.mk
	15
	16	# This has to be exported to make some magic below work.
	17	export DH_OPTIONS
	18
	19	CFLAGS = -Wall -g -Wno-deprecated
	20
	21	ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
	22	CFLAGS += -O0
	23	else
	24	CFLAGS += -O2
	25	endif
	26	ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
	27	INSTALL_PROGRAM += -s
	28	endif
	29
	30	package = tigr-glimmer
	31
	32	build:build-arch-stamp build-indep-stamp
	33	build-arch-stamp::
	34	dh_testdir
	35	# Add here commands to compile the indep part of the package.
	36	$(MAKE) all
	37	ln -f run-glimmer2 tigr-run-glimmer2
	38	touch build-indep-stamp
	39
	40	MANPAGES=debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1 debian/tigr-long-orfs.1
	41
	42	.SUFFIXES: .1 .sgml
	43
	44	.sgml.1:
	45	docbook-to-man $< > $@
	46
	47	build-indep: $(MANPAGES)
	48	gzip -9c CHANGELOG > changelog.gz
	49	touch build-indep
	50
	51	clean::
	52	dh_testdir
	53	dh_testroot
	54	rm -f build-arch-stamp build-indep-stamp configure-stamp changelog.gz
	55	# Add here commands to clean up after the build process.
	56	-$(MAKE) clean
	57	dh_clean $(MANPAGES) tigr-run-glimmer2

+119

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debian/tigr-adjust.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>Novermber 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	the program lacks a description
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-adjust</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	</para>
	70	</refsect1>
	71	<refsect1>
	72	<title>SEE ALSO</title>
	73	<para>
	74	tigr-glimmer2 (1),
	75	tigr-adjust (1),
	76	tigr-anomaly (1),
	77	tigr-build-icm (1),
	78	tigr-check (1),
	79	tigr-codon-usage (1),
	80	tigr-compare-lists (1),
	81	tigr-extract (1),
	82	tigr-generate (1),
	83	tigr-get-len (1),
	84	tigr-get-putative (1),
	85	tigr-long-orfs (1)
	86	</para>
	87	<para>
	88	http://www.tigr.org/software/glimmer/
	89	</para>
	90
	91	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	92	</refsect1>
	93	<refsect1>
	94	<title>AUTHOR</title>
	95
	96	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	97	the &debian; system.
	98	</para>
	99
	100	</refsect1>
	101	</refentry>
	102
	103	<!-- Keep this comment at the end of the file
	104	Local variables:
	105	mode: sgml
	106	sgml-omittag:t
	107	sgml-shorttag:t
	108	sgml-minimize-attributes:nil
	109	sgml-always-quote-attributes:t
	110	sgml-indent-step:2
	111	sgml-indent-data:t
	112	sgml-parent-document:nil
	113	sgml-default-dtd-file:nil
	114	sgml-exposed-tags:nil
	115	sgml-local-catalogs:nil
	116	sgml-local-ecat-files:nil
	117	End:
	118	-->

+124

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debian/tigr-anomaly.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	The program lacks a description
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-anomaly</command>
	64	<arg>>dna-file</arg>
	65	<arg>>coord-file</arg>
	66	</cmdsynopsis>
	67	</refsynopsisdiv>
	68	<refsect1>
	69	<title>DESCRIPTION</title>
	70	<para>
	71	</para>
	72
	73	</refsect1>
	74	<refsect1>
	75	<title>OPTIONS</title>
	76	</refsect1>
	77	<refsect1>
	78	<title>SEE ALSO</title>
	79	<para>
	80	tigr-glimmer2 (1),
	81	tigr-adjust (1),
	82	tigr-anomaly (1),
	83	tigr-build-icm (1),
	84	tigr-check (1),
	85	tigr-codon-usage (1),
	86	tigr-compare-lists (1),
	87	tigr-extract (1),
	88	tigr-generate (1),
	89	tigr-get-len (1),
	90	tigr-get-putative (1),
	91	</para>
	92	<para>
	93	http://www.tigr.org/software/glimmer/
	94	</para>
	95
	96	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	97	</refsect1>
	98	<refsect1>
	99	<title>AUTHOR</title>
	100
	101	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	102	the &debian; system.
	103	</para>
	104
	105	</refsect1>
	106	</refentry>
	107
	108	<!-- Keep this comment at the end of the file
	109	Local variables:
	110	mode: sgml
	111	sgml-omittag:t
	112	sgml-shorttag:t
	113	sgml-minimize-attributes:nil
	114	sgml-always-quote-attributes:t
	115	sgml-indent-step:2
	116	sgml-indent-data:t
	117	sgml-parent-document:nil
	118	sgml-default-dtd-file:nil
	119	sgml-exposed-tags:nil
	120	sgml-local-catalogs:nil
	121	sgml-local-ecat-files:nil
	122	End:
	123	-->

+162

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debian/tigr-build-icm.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>Novemver 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER<title>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56	<refpurpose>Ceates and outputs an interpolated Markov model(IMM)</refpurpose>
	57	</refnamediv>
	58	<refsynopsisdiv>
	59	<cmdsynopsis>
	60	<command>tigr-build-icm</command>
	61	</cmdsynopsis>
	62	</refsynopsisdiv>
	63	<refsect1>
	64	<title>DESCRIPTION</title>
	65	<para>
	66	Program build-icm.c creates and outputs an interpolated Markov
	67	model (IMM) as described in the paper
	68	A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.
	69	Improved Microbial Gene Identification with Glimmer.
	70	Nucleic Acids Research, 1999, in press.
	71	Please reference this paper if you use the system as part of any
	72	published research.
	73	</para><para>
	74	Input comes from the file named on the command-line. Format should be
	75	one string per line. Each line has an ID string followed by white space
	76	followed by the sequence itself. The script run-glimmer2 generates
	77	an input file in the correct format using the 'extract' program.
	78	</para><para>
	79	The IMM is constructed as follows: For a given context, say
	80	acgtta, we want to estimate the probability distribution of the
	81	next character. We shall do this as a linear combination of the
	82	observed probability distributions for this context and all of
	83	its suffixes, i.e., cgtta, gtta, tta, ta, a and empty. By
	84	observed distributions I mean the counts of the number of
	85	occurrences of these strings in the training set. The linear
	86	combination is determined by a set of probabilities, lambda, one
	87	for each context string. For context acgtta the linear combination
	88	coefficients are:
	89	</para><para>
	90	lambda (acgtta)
	91	(1 - lambda (acgtta)) x lambda (cgtta)
	92	(1 - lambda (acgtta)) x (1 - lambda (cgtta)) x lambda (gtta)
	93	(1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta)
	94	(1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta))
	95	x (1 - lambda (tta)) x (1 - lambda (ta)) x (1 - lambda (a))
	96	</para><para>
	97	We compute the lambda values for each context as follows:
	98	- If the number of observations in the training set is >= the constant
	99	SAMPLE_SIZE_BOUND, the lambda for that context is 1.0
	100	- Otherwise, do a chi-square test on the observations for this context
	101	compared to the distribution predicted for the one-character shorter
	102	suffix context.
	103	If the chi-square significance < 0.5, set the lambda for this context to 0.0
	104	Otherwise set the lambda for this context to:
	105	(chi-square significance) x (# observations) / SAMPLE_WEIGHT
	106	</para><para>
	107	To run the program:
	108	</para><para>
	109	build-icm <train.seq > train.model
	110	</para><para>
	111	This will use the training data in train.seq to produce the file
	112	train.model, containing your IMM.
	113	</para>
	114	</refsect1>
	115	<refsect1>
	116	<title>SEE ALSO</title>
	117	<para>
	118	tigr-glimmer2 (1),
	119	tigr-long-orfs (1),
	120	tigr-adjust (1),
	121	tigr-anomaly (1),
	122	tigr-extract (1),
	123	tigr-check (1),
	124	tigr-codon-usage (1),
	125	tigr-compare-lists (1),
	126	tigr-extract (1),
	127	tigr-generate (1),
	128	tigr-get-len (1),
	129	tigr-get-putative (1),
	130	</para>
	131	<para>http://www.tigr.org/software/glimmer/</para>
	132	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	133	</refsect1>
	134	<refsect1>
	135	<title>AUTHOR</title>
	136
	137	<para>This manual page was quickly copied from the glimmer web site and readme file by &dhusername; &dhemail; for
	138	the &debian; system.
	139	</para>
	140
	141	</refsect1>
	142	</refentry>
	143
	144	<!-- Keep this comment at the end of the file
	145	Local variables:
	146	mode: sgml
	147	sgml-omittag:t
	148	sgml-shorttag:t
	149	sgml-minimize-attributes:nil
	150	sgml-always-quote-attributes:t
	151	sgml-indent-step:2
	152	sgml-indent-data:t
	153	sgml-parent-document:nil
	154	sgml-default-dtd-file:nil
	155	sgml-exposed-tags:nil
	156	sgml-local-catalogs:nil
	157	sgml-local-ecat-files:nil
	158	End:
	159	-->
	160
	161

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debian/tigr-check.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	The program lacks a description.
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-check</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	</para>
	70	</refsect1>
	71	<refsect1>
	72	<title>SEE ALSO</title>
	73	<para>
	74	tigr-glimmer2 (1),
	75	tigr-adjust (1),
	76	tigr-anomaly (1),
	77	tigr-build-icm (1),
	78	tigr-check (1),
	79	tigr-codon-usage (1),
	80	tigr-compare-lists (1),
	81	tigr-extract (1),
	82	tigr-generate (1),
	83	tigr-get-len (1),
	84	tigr-get-putative (1),
	85	</para>
	86	<para>
	87	http://www.tigr.org/software/glimmer/
	88	</para>
	89
	90	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	91	</refsect1>
	92	<refsect1>
	93	<title>AUTHOR</title>
	94
	95	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	96	the &debian; system.
	97	</para>
	98
	99	</refsect1>
	100	</refentry>
	101
	102	<!-- Keep this comment at the end of the file
	103	Local variables:
	104	mode: sgml
	105	sgml-omittag:t
	106	sgml-shorttag:t
	107	sgml-minimize-attributes:nil
	108	sgml-always-quote-attributes:t
	109	sgml-indent-step:2
	110	sgml-indent-data:t
	111	sgml-parent-document:nil
	112	sgml-default-dtd-file:nil
	113	sgml-exposed-tags:nil
	114	sgml-local-catalogs:nil
	115	sgml-local-ecat-files:nil
	116	End:
	117	-->

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debian/tigr-codon-usage.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	The program lacks a description
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-codon-usage</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	</para>
	70
	71	</refsect1>
	72	<refsect1>
	73	<title>OPTIONS</title>
	74	</refsect1>
	75	<refsect1>
	76	<title>SEE ALSO</title>
	77	<para>
	78	tigr-glimmer2 (1),
	79	tigr-adjust (1),
	80	tigr-anomaly (1),
	81	tigr-build-icm (1),
	82	tigr-check (1),
	83	tigr-codon-usage (1),
	84	tigr-compare-lists (1),
	85	tigr-extract (1),
	86	tigr-generate (1),
	87	tigr-get-len (1),
	88	tigr-get-putative (1),
	89	</para>
	90	<para>
	91	http://www.tigr.org/software/glimmer/
	92	</para>
	93
	94	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	95	</refsect1>
	96	<refsect1>
	97	<title>AUTHOR</title>
	98
	99	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	100	the &debian; system.
	101	</para>
	102
	103	</refsect1>
	104	</refentry>
	105
	106	<!-- Keep this comment at the end of the file
	107	Local variables:
	108	mode: sgml
	109	sgml-omittag:t
	110	sgml-shorttag:t
	111	sgml-minimize-attributes:nil
	112	sgml-always-quote-attributes:t
	113	sgml-indent-step:2
	114	sgml-indent-data:t
	115	sgml-parent-document:nil
	116	sgml-default-dtd-file:nil
	117	sgml-exposed-tags:nil
	118	sgml-local-catalogs:nil
	119	sgml-local-ecat-files:nil
	120	End:
	121	-->

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debian/tigr-compare-lists.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	unknown
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-compare-lists</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	</para>
	70
	71	</refsect1>
	72	<refsect1>
	73	<title>OPTIONS</title>
	74	</refsect1>
	75	<refsect1>
	76	<title>SEE ALSO</title>
	77	<para>
	78	tigr-glimmer2 (1),
	79	tigr-adjust (1),
	80	tigr-anomaly (1),
	81	tigr-build-icm (1),
	82	tigr-check (1),
	83	tigr-codon-usage (1),
	84	tigr-compare-lists (1),
	85	tigr-extract (1),
	86	tigr-generate (1),
	87	tigr-get-len (1),
	88	tigr-get-putative (1),
	89	</para>
	90	<para>
	91	http://www.tigr.org/software/glimmer/
	92	</para>
	93
	94	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	95	</refsect1>
	96	<refsect1>
	97	<title>AUTHOR</title>
	98
	99	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	100	the &debian; system.
	101	</para>
	102
	103	</refsect1>
	104	</refentry>
	105
	106	<!-- Keep this comment at the end of the file
	107	Local variables:
	108	mode: sgml
	109	sgml-omittag:t
	110	sgml-shorttag:t
	111	sgml-minimize-attributes:nil
	112	sgml-always-quote-attributes:t
	113	sgml-indent-step:2
	114	sgml-indent-data:t
	115	sgml-parent-document:nil
	116	sgml-default-dtd-file:nil
	117	sgml-exposed-tags:nil
	118	sgml-local-catalogs:nil
	119	sgml-local-ecat-files:nil
	120	End:
	121	-->

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debian/tigr-extract.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	Fine start/stop positions of genes in genome sequence
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-extract</command>
	64	<arg>genome-file <option><replaceable>options</replaceable></option></arg>
	65	</cmdsynopsis>
	66	</refsynopsisdiv>
	67	<refsect1>
	68	<title>DESCRIPTION</title>
	69	<para>
	70	Program extract takes a FASTA format sequence file and a file
	71	with a list of start/stop positions in that file (e.g., as produced
	72	by the long-orfs program) and extracts and outputs the
	73	specified sequences.
	74	</para><para>
	75	The first command-line argument is the name of the sequence file,
	76	which must be in FASTA format.
	77	</para><para>
	78	The second command-line argument is the name of the coordinate file.
	79	It must contain a list of pairs of positions in the first file, one
	80	per line. The format of each entry is:
	81	</para><para> <IDstring>> <start position> <stop position>
	82	</para><para>This file should contain no other information, so if you're using
	83	the output of glimmer or long-orfs , you'll have to cut off
	84	header lines.
	85	</para><para>
	86	The output of the program goes to the standard output and has one
	87	line for each line in the coordinate file. Each line contains
	88	the IDstring , followed by white space, followed by the substring
	89	of the sequence file specified by the coordinate pair. Specifically,
	90	the substring starts at the first position of the pair and ends at
	91	the second position (inclusive). If the first position is bigger
	92	than the second, then the DNA reverse complement of each position
	93	is generated. Start/stop pairs that "wrap around" the end of the
	94	genome are allowed.
	95	</para>
	96	</refsect1>
	97	<refsect1>
	98	<title>OPTIONS</title>
	99	<variablelist>
	100	<varlistentry>
	101	<term><option>-skip</option></term>
	102	<listitem>
	103	<para> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</para>
	104	</listitem>
	105	</varlistentry>
	106	<varlistentry>
	107	<term><option>-l</option></term><listitem><para>
	108	makes the output omit an sequences shorter than n characters.
	109	n includes the 3 skipped characters if the -skip switch
	110	is one.
	111	</para></listitem>
	112	</varlistentry>
	113	</variablelist>
	114	</refsect1>
	115	<refsect1>
	116	<title>SEE ALSO</title>
	117	<para>
	118	tigr-glimmer2 (1),
	119	tigr-long-orfs (1),
	120	tigr-adjust (1),
	121	tigr-anomaly (1),
	122	tigr-build-icm (1),
	123	tigr-check (1),
	124	tigr-codon-usage (1),
	125	tigr-compare-lists (1),
	126	tigr-extract (1),
	127	tigr-generate (1),
	128	tigr-get-len (1),
	129	tigr-get-putative (1),
	130	</para>
	131	<para>
	132	http://www.tigr.org/software/glimmer/
	133	</para>
	134
	135	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	136	</refsect1>
	137	<refsect1>
	138	<title>AUTHOR</title>
	139
	140	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	141	the &debian; system.
	142	</para>
	143
	144	</refsect1>
	145	</refentry>
	146
	147	<!-- Keep this comment at the end of the file
	148	Local variables:
	149	mode: sgml
	150	sgml-omittag:t
	151	sgml-shorttag:t
	152	sgml-minimize-attributes:nil
	153	sgml-always-quote-attributes:t
	154	sgml-indent-step:2
	155	sgml-indent-data:t
	156	sgml-parent-document:nil
	157	sgml-default-dtd-file:nil
	158	sgml-exposed-tags:nil
	159	sgml-local-catalogs:nil
	160	sgml-local-ecat-files:nil
	161	End:
	162	-->
	163
	164

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debian/tigr-generate.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	This program lacks a description.
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-generate</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	</para>
	70	</refsect1>
	71	<refsect1>
	72	<title>SEE ALSO</title>
	73	<para>
	74	tigr-glimmer2 (1),
	75	tigr-adjust (1),
	76	tigr-anomaly (1),
	77	tigr-build-icm (1),
	78	tigr-check (1),
	79	tigr-codon-usage (1),
	80	tigr-compare-lists (1),
	81	tigr-extract (1),
	82	tigr-generate (1),
	83	tigr-get-len (1),
	84	tigr-get-putative (1),
	85	</para>
	86	<para>
	87	http://www.tigr.org/software/glimmer/
	88	</para>
	89
	90	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	91	</refsect1>
	92	<refsect1>
	93	<title>AUTHOR</title>
	94
	95	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	96	the &debian; system.
	97	</para>
	98
	99	</refsect1>
	100	</refentry>
	101
	102	<!-- Keep this comment at the end of the file
	103	Local variables:
	104	mode: sgml
	105	sgml-omittag:t
	106	sgml-shorttag:t
	107	sgml-minimize-attributes:nil
	108	sgml-always-quote-attributes:t
	109	sgml-indent-step:2
	110	sgml-indent-data:t
	111	sgml-parent-document:nil
	112	sgml-default-dtd-file:nil
	113	sgml-exposed-tags:nil
	114	sgml-local-catalogs:nil
	115	sgml-local-ecat-files:nil
	116	End:
	117	-->

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debian/tigr-get-len.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	This program lacks a description.
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-get-len</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	</para>
	70	</refsect1>
	71	<refsect1>
	72	<title>SEE ALSO</title>
	73	<para>
	74	tigr-glimmer2 (1),
	75	tigr-adjust (1),
	76	tigr-anomaly (1),
	77	tigr-build-icm (1),
	78	tigr-check (1),
	79	tigr-codon-usage (1),
	80	tigr-compare-lists (1),
	81	tigr-extract (1),
	82	tigr-generate (1),
	83	tigr-get-len (1),
	84	tigr-get-putative (1),
	85	</para>
	86	<para>
	87	http://www.tigr.org/software/glimmer/
	88	</para>
	89
	90	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	91	</refsect1>
	92	<refsect1>
	93	<title>AUTHOR</title>
	94
	95	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	96	the &debian; system.
	97	</para>
	98
	99	</refsect1>
	100	</refentry>
	101
	102	<!-- Keep this comment at the end of the file
	103	Local variables:
	104	mode: sgml
	105	sgml-omittag:t
	106	sgml-shorttag:t
	107	sgml-minimize-attributes:nil
	108	sgml-always-quote-attributes:t
	109	sgml-indent-step:2
	110	sgml-indent-data:t
	111	sgml-parent-document:nil
	112	sgml-default-dtd-file:nil
	113	sgml-exposed-tags:nil
	114	sgml-local-catalogs:nil
	115	sgml-local-ecat-files:nil
	116	End:
	117	-->

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debian/tigr-get-putative.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56	<refpurpose>
	57	</refpurpose>
	58	</refnamediv>
	59	<refsynopsisdiv>
	60	<cmdsynopsis>
	61	<command>tigr-get-putative</command>
	62	</cmdsynopsis>
	63	</refsynopsisdiv>
	64	<refsect1>
	65	<title>DESCRIPTION</title>
	66	</refsect1>
	67	<refsect1>
	68	<title>SEE ALSO</title>
	69	<para>
	70	tigr-glimmer2 (1),
	71	tigr-adjust (1),
	72	tigr-anomaly (1),
	73	tigr-build-icm (1),
	74	tigr-check (1),
	75	tigr-codon-usage (1),
	76	tigr-compare-lists (1),
	77	tigr-extract (1),
	78	tigr-generate (1),
	79	tigr-get-len (1),
	80	tigr-get-putative (1),
	81	tigr-long-orfs (1),
	82	</para>
	83	<para>
	84	http://www.tigr.org/software/glimmer/
	85	</para>
	86	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	87	</refsect1>
	88	<refsect1>
	89	<title>AUTHOR</title>
	90
	91	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	92	the &debian; system.
	93	</para>
	94
	95	</refsect1>
	96	</refentry>
	97
	98	<!-- Keep this comment at the end of the file
	99	Local variables:
	100	mode: sgml
	101	sgml-omittag:t
	102	sgml-shorttag:t
	103	sgml-minimize-attributes:nil
	104	sgml-always-quote-attributes:t
	105	sgml-indent-step:2
	106	sgml-indent-data:t
	107	sgml-parent-document:nil
	108	sgml-default-dtd-file:nil
	109	sgml-exposed-tags:nil
	110	sgml-local-catalogs:nil
	111	sgml-local-ecat-files:nil
	112	End:
	113	-->

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debian/tigr-glimmer2.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56	<refpurpose>
	57	Find/Score potential genes in genome-file using the probability model in icm-file
	58	</refpurpose>
	59	</refnamediv>
	60	<refsynopsisdiv>
	61	<cmdsynopsis>
	62	<command>tigr-glimmer2</command>
	63	<arg><option><replaceable>genome-file</replaceable></option></arg>
	64	<arg><option><replaceable>icm-file</replaceable></option></arg>
	65	<arg><option><replaceable>[options]</replaceable></option></arg>
	66	</cmdsynopsis>
	67	</refsynopsisdiv>
	68	<refsect1>
	69	<title>DESCRIPTION</title>
	70	<para>
	71	<command>&dhpackage;</command> is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. <command>&dhpackage;</command> (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on <command>&dhpackage;</command> 1.0 and in our subsequent paper on <command>&dhpackage;</command> 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. <command>&dhpackage;</command> 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
	72	</para><para>
	73	<command>&dhpackage;</command> is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site.
	74	</para><para>
	75	A special version of <command>&dhpackage;</command> designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system.
	76	</para><para>
	77	The <command>&dhpackage;</command> system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. <command>&dhpackage;</command> automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far.
	78	<command>&dhpackage;</command> is a program that...</para>
	79	</refsect1>
	80	<refsect1>
	81	<title>OPTIONS</title>
	82	<variablelist>
	83	<varlistentry>
	84	<term><option>-C <replaceable>n</replaceable></option></term>
	85	<listitem>
	86	<para>Use n as GC percentage of independent model</para>
	87	<para>Note: n should be a percentage, e.g., -C 45.2</para>
	88	</listitem>
	89	</varlistentry>
	90	<varlistentry>
	91	<term>-f</term><listitem><para>Use ribosome-binding energy to choose start codon</para></listitem>
	92	</varlistentry>
	93	<varlistentry>
	94	<term><option>+f</option></term><listitem><para>Use first codon in orf as start codon</para></listitem>
	95	</varlistentry>
	96	<varlistentry>
	97	<term><option>-g <replaceable>n</replaceable></option></term><listitem><para>Set minimum gene length to n</para></listitem>
	98	</varlistentry>
	99	<varlistentry>
	100	<term><option>-i <replaceable>filename</replaceable></option></term>
	101	<listitem>
	102	<para>Use <option><replaceable>filename</replaceable></option>
	103	to select regions of bases that are off
	104	limits, so that no bases within that area will be examined
	105	</para>
	106	</listitem>
	107	</varlistentry>
	108	<varlistentry>
	109	<term><option>-l</option></term>
	110	<listitem><para>Assume linear rather than circular genome, i.e., no wraparound</para></listitem>
	111	</varlistentry>
	112	<varlistentry>
	113	<term><option>-L <replaceable>filename</replaceable></option></term>
	114	<listitem><para>Use filename to specify a list of orfs that should
	115	be scored separately, with no overlap rules
	116	</para></listitem>
	117	</varlistentry>
	118	<varlistentry>
	119	<term><option>-M</option></term>
	120	<listitem><para>Input is a multifasta file of separate genes to be scored
	121	separately, with no overlap rules
	122	</para>
	123	</listitem>
	124	</varlistentry>
	125	<varlistentry>
	126	<term><option>-o <replaceable>n</replaceable></option></term>
	127	<listitem>
	128	<para>Set minimum overlap length to n. Overlaps shorter than this
	129	are ignored.
	130	</para></listitem>
	131	</varlistentry>
	132	<varlistentry>
	133	<term><option>-p <replaceable>n</replaceable></option></term>
	134	<listitem>
	135	<para>
	136	Set minimum overlap percentage to n%. Overlaps shorter than this percentage of both strings are ignored.
	137	</para>
	138	</listitem>
	139	</varlistentry>
	140	<varlistentry>
	141	<term><option>-q <replaceable>n</replaceable></option></term>
	142	<listitem>
	143	<para>Set the maximum length orf that can be rejected because of
	144	the independent probability score column to (n - 1)
	145	</para>
	146	</listitem>
	147	</varlistentry>
	148	<varlistentry>
	149	<term><option>-r</option></term>
	150	<listitem>
	151	<para>
	152	Don't use independent probability score column
	153	</para>
	154	</listitem>
	155	</varlistentry>
	156	<varlistentry>
	157	<term><option>+r</option></term>
	158	<listitem><para>
	159	Use independent probability score column
	160	</para>
	161	</listitem>
	162	</varlistentry>
	163	<varlistentry>
	164	<term><option>-r</option></term>
	165	<listitem>
	166	<para>
	167	Don't use independent probability score column
	168	</para> </listitem> </varlistentry> <varlistentry>
	169	<term><option>-s <replaceable>s</replaceable></option></term>
	170	<listitem><para> Use string s as the ribosome binding pattern to find start codons.</para>
	171	</listitem>
	172	</varlistentry>
	173	<varlistentry>
	174	<term><option>+S</option></term>
	175	<listitem>
	176	<para>
	177	Do use stricter independent intergenic model that doesn't
	178	give probabilities to in-frame stop codons. (Option is obsolete
	179	since this is now the only behaviour
	180	</para> </listitem>
	181	</varlistentry>
	182	<varlistentry>
	183	<term><option>-t <replaceable>n</replaceable></option></term>
	184	<listitem><para>
	185	Set threshold score for calling as gene to n. If the in-frame
	186	score >= n, then the region is given a number and considered
	187	a potential gene.
	188	</para> </listitem>
	189	</varlistentry>
	190	<varlistentry>
	191	<term><option>-w <replaceable>n</replaceable> </option></term>
	192	<listitem><para>
	193	Use "weak" scores on tentative genes n or longer. Weak
	194	scores ignore the independent probability score.
	195	</para></listitem>
	196	</varlistentry>
	197	</variablelist>
	198	</refsect1>
	199	<refsect1>
	200	<title>SEE ALSO</title>
	201	<para>
	202	tigr-adjust (1),
	203	tigr-anomaly (1),
	204	tigr-build-icm (1),
	205	tigr-check (1),
	206	tigr-codon-usage (1),
	207	tigr-compare-lists (1),
	208	tigr-extract (1),
	209	tigr-generate (1),
	210	tigr-get-len (1),
	211	tigr-get-putative (1),
	212	tigr-glimmer2 (1),
	213	tigr-long-orfs (1)
	214	</para>
	215	<para>
	216	http://www.tigr.org/software/glimmer/
	217	</para>
	218	<para>Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.</para>
	219	</refsect1>
	220	<refsect1>
	221	<title>AUTHOR</title>
	222	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	223	the &debian; system.
	224	</para>
	225	</refsect1>
	226	</refentry>
	227
	228	<!-- Keep this comment at the end of the file
	229	Local variables:
	230	mode: sgml
	231	sgml-omittag:t
	232	sgml-shorttag:t
	233	sgml-minimize-attributes:nil
	234	sgml-always-quote-attributes:t
	235	sgml-indent-step:2
	236	sgml-indent-data:t
	237	sgml-parent-document:nil
	238	sgml-default-dtd-file:nil
	239	sgml-exposed-tags:nil
	240	sgml-local-catalogs:nil
	241	sgml-local-ecat-files:nil
	242	End:
	243	-->
	244
	245

+238

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debian/tigr-long-orfs.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>LONG-ORFS</refentrytitle>">
	27	<!ENTITY dhpackage "long-orfs">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	Find/Score potential genes in genome-file using
	59	the probability model in icm-file
	60	</refpurpose>
	61	</refnamediv>
	62	<refsynopsisdiv>
	63	<cmdsynopsis>
	64	<command>tigr-long-orgs</command>
	65	<arg>genome-file <option><replaceable>options</replaceable></option></arg>
	66	</cmdsynopsis>
	67	</refsynopsisdiv>
	68	<refsect1>
	69	<title>DESCRIPTION</title>
	70	<para>
	71	Program long-orfs takes a sequence file (in FASTA format) and
	72	outputs a list of all long "potential genes" in it that do not
	73	overlap by too much. By "potential gene" I mean the portion of
	74	an orf from the first start codon to the stop codon at the end.
	75	</para><para>
	76	The first few lines of output specify the settings of various
	77	parameters in the program:
	78	</para><para>
	79	Minimum gene length is the length of the smallest fragment
	80	considered to be a gene. The length is measured from the first base
	81	of the start codon to the last base before the stop codon.
	82	This value can be specified when running the program with the -g option.
	83	By default, the program now (April 2003) will compute an optimal length
	84	for this parameter, where "optimal" is the value that produces the
	85	greatest number of long ORFs, thereby increasing the amount of data
	86	used for training.
	87	</para><para>
	88	Minimum overlap length is a lower bound on the number of bases overlap
	89	between 2 genes that is considered a problem. Overlaps shorter than
	90	this are ignored.
	91	</para><para>
	92	Minimum overlap percent is another lower bound on the number of bases
	93	overlap that is considered a problem. Overlaps shorter than this
	94	percentage of both genes are ignored.
	95	</para><para>
	96	The next portion of the output is a list of potential genes:
	97	</para><para>
	98	Column 1 is an ID number for reference purposes. It is assigned
	99	sequentially starting with 1 to all long potential genes. If
	100	overlapping genes are eliminated, gaps in the numbers will occur.
	101	The ID prefix is specified in the constant ID_PREFIX .
	102	</para><para>
	103	Column 2 is the position of the first base of the first start codon in
	104	the orf. Currently I use atg, and gtg as start codons. This is
	105	easily changed in the function Is_Start () .
	106	</para><para>
	107	Column 3 is the position of the last base before the stop codon. Stop
	108	codons are taa, tag, and tga. Note that for orfs in the reverse
	109	reading frames have their start position higher than the end position.
	110	The order in which orfs are listed is in increasing order by
	111	Max {OrfStart, End}, i.e., the highest numbered position in the orf,
	112	except for orfs that "wrap around" the end of the sequence.
	113	</para><para>
	114	When two genes with ID numbers overlap by at least a sufficient
	115	amount (as determined by Min_Olap and Min_Olap_Percent ), they
	116	are eliminated and do not appear in the output.
	117	</para><para>
	118	The final output of the program (sent to the standard error file so
	119	it does not show up when output is redirected to a file) is the
	120	length of the longest orf found.
	121	</para><para>
	122
	123
	124	Specifying Different Start and Stop Codons:
	125	</para><para>
	126	To specify different sets of start and stop codons, modify the file
	127	gene.h . Specifically, the functions:
	128	</para><para>
	129	Is_Forward_Start Is_Reverse_Start Is_Start
	130	Is_Forward_Stop Is_Reverse_Stop Is_Stop
	131	</para><para>
	132	are used to determine what is used for start and stop codons.
	133	</para><para>
	134	Is_Start and Is_Stop do simple string comparisons to specify
	135	which patterns are used. To add a new pattern, just add the comparison
	136	for it. To remove a pattern, comment out or delete the comparison
	137	for it.
	138	</para><para>
	139	The other four functions use a bit comparison to determine start and
	140	stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
	141	for each base, one bit for each possible value of the bases, T, G, C
	142	or A. Thus the bit pattern 0010 0101 1100 represents the base
	143	pattern [C] [A or G] [G or T]. By doing bit operations (& \| ~) and
	144	comparisons, more complicated patterns involving ambiguous reads
	145	can be tested efficiently. Simple patterns can be tested as in
	146	the current code.
	147	</para><para>
	148	For example, to insert an additional start codon of CAT requires 3 changes:
	149	1. The line
	150	\|\| (Codon & 0x218) == Codon
	151	should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
	152	represents CAT.
	153	2. The line
	154	\|\| (Codon & 0x184) == Codon
	155	should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
	156	represents ATG, which is the reverse-complement of CAT. Alternately,
	157	the #define constant ATG_MASK could be used.
	158	3. The line
	159	\|\| strncmp (S, "cat", 3) == 0
	160	should be inserted into Is_Start .
	161	</para>
	162
	163	</refsect1>
	164	<refsect1>
	165	<title>OPTIONS</title>
	166	<variablelist>
	167	<varlistentry>
	168	<term><option>-g <replaceable>n</replaceable></option></term>
	169	<listitem>
	170	<para> Set minimum gene length to n. Default is to compute an
	171	optimal value automatically. Don't change this unless you
	172	know what you're doing.</para>
	173	</listitem>
	174	</varlistentry>
	175	<varlistentry>
	176	<term><option>-l</option></term><listitem><para>Regard the genome as linear (not circular), i.e., do not allow
	177	genes to "wrap around" the end of the genome.
	178	This option works on both glimmer and long-orfs .
	179	The default behavior is to regard the genome as circular.</para></listitem>
	180	</varlistentry>
	181	<varlistentry>
	182	<term><option>-o <replaceable>n</replaceable></option></term><listitem><para>Set maximum overlap length to n. Overlaps shorter than this
	183	are permitted. (Default is 0 bp.)</para></listitem>
	184	</varlistentry>
	185	<varlistentry>
	186	<term><option>-p <replaceable>n</replaceable></option></term><listitem><para>Set maximum overlap percentage to n%. Overlaps shorter than
	187	this percentage of both strings are ignored. (Default is 10%.)</para></listitem>
	188	</varlistentry>
	189	</variablelist>
	190	</refsect1>
	191	<refsect1>
	192	<title>SEE ALSO</title>
	193	<para>
	194	tigr-glimmer2 (1),
	195	tigr-adjust (1),
	196	tigr-anomaly (1),
	197	tigr-build-icm (1),
	198	tigr-check (1),
	199	tigr-codon-usage (1),
	200	tigr-compare-lists (1),
	201	tigr-extract (1),
	202	tigr-generate (1),
	203	tigr-get-len (1),
	204	tigr-get-putative (1),
	205	</para>
	206	<para>
	207	http://www.tigr.org/software/glimmer/
	208	</para>
	209
	210	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	211	</refsect1>
	212	<refsect1>
	213	<title>AUTHOR</title>
	214
	215	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	216	the &debian; system.
	217	</para>
	218
	219	</refsect1>
	220	</refentry>
	221
	222	<!-- Keep this comment at the end of the file
	223	Local variables:
	224	mode: sgml
	225	sgml-omittag:t
	226	sgml-shorttag:t
	227	sgml-minimize-attributes:nil
	228	sgml-always-quote-attributes:t
	229	sgml-indent-step:2
	230	sgml-indent-data:t
	231	sgml-parent-document:nil
	232	sgml-default-dtd-file:nil
	233	sgml-exposed-tags:nil
	234	sgml-local-catalogs:nil
	235	sgml-local-ecat-files:nil
	236	End:
	237	-->

+120

-0

debian/tigr-run-glimmer2.sgml less more

	0	<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
	1
	2	<!-- Process this file with docbook-to-man to generate an nroff manual
	3	page: `docbook-to-man manpage.sgml > manpage.1'. You may view
	4	the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
	5	less'. A typical entry in a Makefile or Makefile.am is:
	6
	7	manpage.1: manpage.sgml
	8	docbook-to-man $< > $@
	9
	10
	11	The docbook-to-man binary is found in the docbook-to-man package.
	12	Please remember that if you create the nroff version in one of the
	13	debian/rules file targets (such as build), you will need to include
	14	docbook-to-man in your Build-Depends control field.
	15
	16	-->
	17
	18	<!-- Fill in your name for FIRSTNAME and SURNAME. -->
	19	<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
	20	<!ENTITY dhsurname "<surname>Möller</surname>">
	21	<!-- Please adjust the date whenever revising the manpage. -->
	22	<!ENTITY dhdate "<date>November 10, 2004</date>">
	23	<!ENTITY dhsection "<manvolnum>1</manvolnum>">
	24	<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	Apply the suite of programs within glimmer2 to a a prokaryotic or archean genome.
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-run-glimmer2</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions.
	70	</para>
	71	</refsect1>
	72	<refsect1>
	73	<title>SEE ALSO</title>
	74	<para>
	75	tigr-glimmer2 (1),
	76	tigr-adjust (1),
	77	tigr-anomaly (1),
	78	tigr-build-icm (1),
	79	tigr-check (1),
	80	tigr-codon-usage (1),
	81	tigr-compare-lists (1),
	82	tigr-extract (1),
	83	tigr-generate (1),
	84	tigr-get-len (1),
	85	tigr-get-putative (1),
	86	tigr-long-orfs (1),
	87	</para>
	88	<para>
	89	http://www.tigr.org/software/glimmer/
	90	</para>
	91
	92	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	93	</refsect1>
	94	<refsect1>
	95	<title>AUTHOR</title>
	96
	97	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	98	the &debian; system.
	99	</para>
	100
	101	</refsect1>
	102	</refentry>
	103
	104	<!-- Keep this comment at the end of the file
	105	Local variables:
	106	mode: sgml
	107	sgml-omittag:t
	108	sgml-shorttag:t
	109	sgml-minimize-attributes:nil
	110	sgml-always-quote-attributes:t
	111	sgml-indent-step:2
	112	sgml-indent-data:t
	113	sgml-parent-document:nil
	114	sgml-default-dtd-file:nil
	115	sgml-exposed-tags:nil
	116	sgml-local-catalogs:nil
	117	sgml-local-ecat-files:nil
	118	End:
	119	-->

-0

debian/watch less more

	0	# format version number, currently 2; this line is compulsory!
	1	version=2
	2
	3	# This is one format for an HTTP site, which is the same as the FTP format
	4	ftp://ftp.tigr.org/pub/software/Glimmer/glimmer(\d+).tar.gz

-3

delcher.h less more

17	17
18	18	#include <stdio.h>
19	19	#include <stdlib.h>
20		#include <iostream.h>
21		#include <iomanip.h>
22		#include <fstream.h>
	20	#include <iostream>
	21	#include <iomanip>
	22	#include <fstream>
23	23	#include <math.h>
24	24	#include <string.h>
25	25	#include <ctype.h>

30	30	#include <errno.h>
31	31	#include <unistd.h>
32	32
	33	using namespace std;
33	34
34	35	#define TRUE 1
35	36	#define FALSE 0

-4

run-glimmer2 less more

	0	#!/bin/sh
0	1	echo "run Glimmer2"
1	2	clear
2	3	echo "Genome is " $1
3	4	echo "Find non-overlapping orfs in tmp.coord"
4	5	rm -f tmp.coord
5		long-orfs $1 \| get-putative >tmp.coord
	6	tigr-long-orfs $1 \| tigr-get-putative >tmp.coord
6	7	echo "Extract training sequences to tmp.train"
7	8	rm -f tmp.train
8		extract $1 tmp.coord >tmp.train
	9	tigr-extract $1 tmp.coord >tmp.train
9	10	wc tmp.train
10	11	echo "Build interpolated context model in tmp.model"
11	12	rm -f tmp.model
12		build-icm <tmp.train >tmp.model
	13	tigr-build-icm <tmp.train >tmp.model
13	14	echo "Predict genes with Glimmer2 with coordinates in g2.coord"
14	15	rm -f g2.coord
15		glimmer2 $1 tmp.model \| get-putative >g2.coord
	16	tigr-glimmer2 $1 tmp.model \| tigr-get-putative >g2.coord