Commit 663ad510cf33ec8bd60ea9c03f8df448556dd8de - tigr-glimmer

Removed man pages that belong to old executables Andreas Tille 16 years ago

9 changed file(s) with 0 addition(s) and 1022 deletion(s). Raw diff Collapse all Expand all

-190

~~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		...\"
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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		glimmer3 (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 Glimmer3.
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

-1

~~debian/manpages.links~~ less more

tigr-glimmer glimmer2

-119

~~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-glimmer3 (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 Glimmer3.</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		-->

-118

~~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-glimmer3 (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 Glimmer3.</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		-->

-122

~~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-glimmer3 (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 Glimmer3.</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		-->

-122

~~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-glimmer3 (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 Glimmer3.</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		-->

-118

~~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-glimmer3 (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 Glimmer3.</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		-->

-118

~~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-glimmer3 (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 Glimmer3.</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		-->

-114

~~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-glimmer3 (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 Glimmer3.</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		-->