Package list tigr-glimmer / 663ad51
Removed man pages that belong to old executables Andreas Tille 13 years ago
9 changed file(s) with 0 addition(s) and 1022 deletion(s). Raw diff Collapse all Expand all
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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
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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\"
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41 .el .ie !\\*(f1 \{\
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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 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
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debian/manpages.links less more
0 tigr-glimmer glimmer2
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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-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 -->
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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-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 -->
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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-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 -->
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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-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 -->
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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-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 -->
+0
-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 -->
+0
-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 -->