[med-svn] [seqtools] 03/04: Add manpages

Andreas Tille tille at debian.org
Thu Oct 26 11:11:36 UTC 2017 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository seqtools.

commit 0995825feb3fe516ddb59b850670b9a0104f5ee5
Author: Andreas Tille <tille at debian.org>
Date:   Thu Oct 26 12:57:32 2017 +0200

    Add manpages
---
 debian/belvu.1         | 154 ++++++++++++++++++++++++++++++++++++++++++
 debian/belvu.manpages  |   1 +
 debian/blixem.1        | 178 +++++++++++++++++++++++++++++++++++++++++++++++++
 debian/blixem.manpages |   1 +
 debian/blixemh.1       | 178 +++++++++++++++++++++++++++++++++++++++++++++++++
 debian/createmanpages  |  40 +++++++++++
 debian/dotter.1        | 148 ++++++++++++++++++++++++++++++++++++++++
 debian/dotter.manpages |   1 +
 8 files changed, 701 insertions(+)

diff --git a/debian/belvu.1 b/debian/belvu.1
new file mode 100644
index 0000000..05df917
--- /dev/null
+++ b/debian/belvu.1
@@ -0,0 +1,154 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH BELVU "1" "October 2017" "belvu 4.44.1" "User Commands"
+.SH NAME
+belvu \- View multiple alignments in good-looking colours
+.SH DESCRIPTION
+.IP
+Belvu \- View multiple alignments in good\-looking colours.
+.IP
+Usage: belvu [options] <multiple_alignment>|\-
+.IP
+<multiple_alignment>|\- = alignment file or pipe.
+.IP
+Options:
+.TP
+\fB\-c\fR
+Print Conservation table.
+.TP
+\fB\-l\fR <file>
+Load residue color code file.
+.TP
+\fB\-L\fR <file>
+Load markup and organism color code file.
+.TP
+\fB\-m\fR <file>
+Read file with matching sequence segments.
+.TP
+\fB\-r\fR
+Read alignment in 'raw' format (Name sequence).
+.TP
+\fB\-R\fR
+Do not parse coordinates when reading alignment.
+.HP
+\fB\-o\fR <format> Write alignment or tree to stdout in this format and exit.
+.IP
+Valid formats: MSF, Mul(Stockholm), Selex,
+FastaAlign, Fasta, tree.
+.HP
+\fB\-X\fR <cutoff> Print UPGMA\-based subfamilies at cutoff <cutoff>.
+.HP
+\fB\-n\fR <cutoff> Make non\-redundant to <cutoff> %identity at startup.
+.HP
+\fB\-Q\fR <cutoff> Remove columns more gappy than <cutoff>.
+.HP
+\fB\-q\fR <cutoff> Remove sequences more gappy than <cutoff>.
+.TP
+\fB\-G\fR
+Penalize gaps in pairwise comparisons.
+.TP
+\fB\-i\fR
+Ignore gaps in conservation calculation.
+.TP
+\fB\-P\fR
+Remove partial sequences at startup.
+.TP
+\fB\-C\fR
+Don't write coordinates to saved file.
+.TP
+\fB\-z\fR <char>
+Separator char between name and coordinates in saved file.
+.TP
+\fB\-a\fR
+Show alignment annotations on screen (Stockholm format only).
+.TP
+\fB\-p\fR
+Output random model probabilites for HMMER.
+(Based on all residues.)
+.TP
+\fB\-S\fR <order>
+Sort sequences in this order.
+.IP
+a \-> alphabetically
+o \-> by Swissprot organism, alphabetically
+s \-> by score
+n \-> by Neighbor\-joining tree
+u \-> by UPGMA tree
+S \-> by similarity to first sequence
+i \-> by identity to first sequence
+.TP
+\fB\-s\fR <file>
+Read in file of scores.
+.HP
+\fB\-T\fR <method> Tree options:
+.IP
+i \-> Start up showing tree
+I \-> Start up showing only tree
+d \-> Show distances in tree
+n \-> Neighbor\-joining
+u \-> UPGMA
+c \-> Don't color tree by organism
+o \-> Don't display sequence coordinates in tree
+b \-> Use Scoredist distance correction (default)
+j \-> Use Jukes\-Cantor distance correction
+k \-> Use Kimura distance correction
+s \-> Use Storm & Sonnhammer distance correction
+r \-> Use uncorrected distances
+p \-> Print distance matrix and exit
+R \-> Read distance matrix instead of alignment
+.IP
+(only in combination with Tree routines)
+.TP
+\fB\-b\fR <n>
+Apply boostrap analysis with <n> bootstrap samples
+.TP
+\fB\-B\fR
+Print out bootstrap trees and exit
+(Negative value \-> display bootstrap trees on screen)
+.TP
+\fB\-O\fR <label>
+Read organism info after this label (default OS)
+.TP
+\fB\-t\fR <title>
+Set window title.
+.TP
+\fB\-u\fR
+Start up with uncoloured alignment (faster).
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show more detailed usage information
+.TP
+\fB\-\-compiled\fR
+Show package compile date
+.TP
+\fB\-\-version\fR
+Show package version number
+.TP
+\fB\-\-abbrev\-title\-on\fR
+Abbreviate window title prefixes
+.TP
+\fB\-\-abbrev\-title\-off\fR
+Do not abbreviate window title prefixes
+.IP
+setenv BELVU_FETCH to desired sequence fetching program.
+setenv BELVU_FONT_SIZE to specify window font size.
+setenv BELVU_STATUSBAR_SIZE to specify statusbar font size (0 => hide statusbar).
+.PP
+\fB\-\-\-\-\-\fR
+.IP
+Written by Gemma Barson <gb10 at sanger.ac.uk>
+Based on original code by Erik Sonnhammer <Erik.Sonnhammer at sbc.su.se>
+.IP
+Reference: Scoredist: A simple and robust protein sequence distance estimator.
+.IP
+Erik LL Sonnhammer and Volker Hollich.
+BMC Bioinformatics 6:108 (2005)
+.IP
+See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
+.IP
+Copyright (c) 2011\-2015: Genome Research Ltd.
+Belvu is distributed under the GNU Public License; see http://www.gnu.org/copyleft/gpl.txt
+.TP
+Version 4.44.1
+14:27:56 Oct 19 2017
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/belvu.manpages b/debian/belvu.manpages
new file mode 100644
index 0000000..afc297c
--- /dev/null
+++ b/debian/belvu.manpages
@@ -0,0 +1 @@
+debian/belvu.1
diff --git a/debian/blixem.1 b/debian/blixem.1
new file mode 100644
index 0000000..e2b8084
--- /dev/null
+++ b/debian/blixem.1
@@ -0,0 +1,178 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH BLIXEM "1" "October 2017" "blixem 4.44.1" "User Commands"
+.SH NAME
+blixem \- display multiple alignments against a reference sequence
+.SH DESCRIPTION
+.IP
+Blixem \- display multiple alignments against a reference sequence.
+.IP
+Usage: blixem [options] [<sequence_file>] <data_file> [X options]
+.IP
+<sequence_file> contains the reference sequence in FASTA format.
+<data_file> is a GFF v3 file containing alignments and other features.
+If <sequence_file> is ommitted, <data_file> should contain the reference
+sequence in FASTA format, below a comment line that reads ##FASTA.
+.IP
+Both <sequence_file> and <data_file> can be substituted by "\-"
+for reading from stdin (pipe).  If <sequence_file> is piped, the first
+line should contain the sequence name and the second the sequence itself.
+.IP
+Options:
+.TP
+\fB\-t\fR <type>, \fB\-\-display\-type=\fR<type>
+MANDATORY
+.IP
+Whether to display sequences in nucleotide or protein mode. Must be one of:
+.IP
+N = nucleotide
+P = protein
+.HP
+\fB\-a\fR <names>, \fB\-\-alignment\-names=\fR<names>
+.IP
+Specify a string giving the names of the alignments, e.g. "EST_mouse EST_human" etc.
+.HP
+\fB\-c\fR <file>, \fB\-\-config\-file=\fR<file>
+.IP
+Read configuration options from 'file'.
+.HP
+\fB\-\-abbrev\-title\-on\fR
+.IP
+Abbreviate window title prefixes
+.HP
+\fB\-\-abbrev\-title\-off\fR
+.IP
+Do not abbreviate window title prefixes
+.HP
+\fB\-\-compiled\fR
+.IP
+Show package compile date.
+.HP
+\fB\-d\fR <data_file>, \fB\-\-data\-file=\fR<data_file>
+.IP
+Alternative way of specifying <data_file> using an argument
+.HP
+\fB\-\-dataset\fR
+.IP
+Optional string to indicate a data\-set that the alignments are from.
+.HP
+\fB\-e\fR <sequence_file>, \fB\-\-sequence\-file=\fR<sequence_file>
+.IP
+Alternative way of specifying <sequence_file> using an argument
+.HP
+\fB\-\-dotter\-first\-match\fR
+.IP
+Call Dotter on the first match to the right of the default start coord.
+.HP
+\fB\-\-fetch\-server\fR <nodeid:port>
+.IP
+Causes Blixem to get sequences from a fetch server at machine 'nodeid' on the given
+port (default 22100).
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+More detailed usage information.
+.HP
+\fB\-\-hide\-big\-picture\fR
+.IP
+Hide the big picture section on start\-up.
+.HP
+\fB\-\-hide\-inactive\-strand\fR
+.IP
+Hide the inactive strand (i.e. the reverse strand, or the forward strand if the \fB\-R\fR option
+is used).
+.HP
+\fB\-\-highlight\-diffs\fR
+.IP
+Enable 'highlight differences' mode, where mismatches (rather than matches) are highlighted.
+.HP
+\fB\-\-invert\-sort\fR
+.IP
+Invert sorting order
+.HP
+\fB\-m\fR <from[:to]>, \fB\-\-map\-coords=\fR<from[:to]>
+.IP
+Map the coordinate system so that the given 'from' coordinate maps to the given
+\&'to' coordinate (or to '1' if 'to' is not given).
+.HP
+\fB\-n\fR, \fB\-\-negate\-coords\fR
+.IP
+When showing the reverse strand, negate the display coordinates.
+.HP
+\fB\-o\fR <n>, \fB\-\-offset=\fR<n>
+.IP
+Offset the reference sequence coordinate system by n.
+.HP
+\fB\-\-optional\-data\fR
+.IP
+Parse additional data such as organism and tissue\-type on start\-up.
+.HP
+\fB\-\-remove\-input\-files\fR
+.IP
+Delete the input files after they have been parsed.
+.HP
+\fB\-r\fR, \fB\-\-reverse\-strand\fR
+.IP
+Indicates that the given reference sequence is the reverse strand.
+.HP
+\fB\-\-save\-temp\-files\fR
+.IP
+Save any temporary files created by Blixem.
+.HP
+\fB\-\-show\-coverage\fR
+.IP
+Display the coverage section on start\-up.
+.HP
+\fB\-\-sort\-mode=\fR<mode>
+.IP
+Default sort mode. Use \fB\-\-help\fR option to see details.
+.HP
+\fB\-\-squash\-matches\fR
+.IP
+Compress the alignment lists on start\-up.
+.HP
+\fB\-s\fR <n>, \fB\-\-start\-coord=\fR<n>
+.IP
+Start with the display centred on coordinate n.
+.HP
+\fB\-\-start\-next\-match\fR
+.IP
+Start with the display centred on the first match to the right of the default start coord.
+.HP
+\fB\-y\fR <file>, \fB\-\-styles\-file=\fR<file>
+.IP
+Read color options from a key\-value file. Use \fB\-\-help\fR option to see details.
+.HP
+\fB\-\-version\fR
+.IP
+Show package version number.
+.HP
+\fB\-z\fR <start:end>, \fB\-\-zoom\-range=\fR<start:end>
+.IP
+Specify the initial range of coordinates to zoom the big picture in to.
+.HP
+\fB\-\-zoom\-whole\fR
+.IP
+Start with the big picture zoomed out to view the full reference sequence range.
+.IP
+Some X options:
+\fB\-acefont\fR <font> Main font.
+\fB\-font\fR    <font> Menu font.
+.PP
+\fB\-\-\-\-\-\fR
+.IP
+Written by Gemma Barson <gb10 at sanger.ac.uk>
+Based on original code by Erik Sonnhammer <Erik.Sonnhammer at sbc.su.se>
+.IP
+Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale
+.IP
+Sequence Homology Analysis. Comput. Applic. Biosci. 10:301\-307.
+.IP
+See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
+.IP
+Copyright (c) 2009\-2015: Genome Research Ltd.
+Blixem is distributed under the GNU Public License; see http://www.gnu.org/copyleft/gpl.txt
+.TP
+Version 4.44.1
+14:27:56 Oct 19 2017
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/blixem.manpages b/debian/blixem.manpages
new file mode 100644
index 0000000..f4b279d
--- /dev/null
+++ b/debian/blixem.manpages
@@ -0,0 +1 @@
+debian/blixem*.1
diff --git a/debian/blixemh.1 b/debian/blixemh.1
new file mode 100644
index 0000000..3a195cc
--- /dev/null
+++ b/debian/blixemh.1
@@ -0,0 +1,178 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH BLIXEMH "1" "October 2017" "blixemh 4.44.1" "User Commands"
+.SH NAME
+blixemh \- display multiple alignments against a reference sequence
+.SH DESCRIPTION
+.IP
+Blixem \- display multiple alignments against a reference sequence.
+.IP
+Usage: blixem [options] [<sequence_file>] <data_file> [X options]
+.IP
+<sequence_file> contains the reference sequence in FASTA format.
+<data_file> is a GFF v3 file containing alignments and other features.
+If <sequence_file> is ommitted, <data_file> should contain the reference
+sequence in FASTA format, below a comment line that reads ##FASTA.
+.IP
+Both <sequence_file> and <data_file> can be substituted by "\-"
+for reading from stdin (pipe).  If <sequence_file> is piped, the first
+line should contain the sequence name and the second the sequence itself.
+.IP
+Options:
+.TP
+\fB\-t\fR <type>, \fB\-\-display\-type=\fR<type>
+MANDATORY
+.IP
+Whether to display sequences in nucleotide or protein mode. Must be one of:
+.IP
+N = nucleotide
+P = protein
+.HP
+\fB\-a\fR <names>, \fB\-\-alignment\-names=\fR<names>
+.IP
+Specify a string giving the names of the alignments, e.g. "EST_mouse EST_human" etc.
+.HP
+\fB\-c\fR <file>, \fB\-\-config\-file=\fR<file>
+.IP
+Read configuration options from 'file'.
+.HP
+\fB\-\-abbrev\-title\-on\fR
+.IP
+Abbreviate window title prefixes
+.HP
+\fB\-\-abbrev\-title\-off\fR
+.IP
+Do not abbreviate window title prefixes
+.HP
+\fB\-\-compiled\fR
+.IP
+Show package compile date.
+.HP
+\fB\-d\fR <data_file>, \fB\-\-data\-file=\fR<data_file>
+.IP
+Alternative way of specifying <data_file> using an argument
+.HP
+\fB\-\-dataset\fR
+.IP
+Optional string to indicate a data\-set that the alignments are from.
+.HP
+\fB\-e\fR <sequence_file>, \fB\-\-sequence\-file=\fR<sequence_file>
+.IP
+Alternative way of specifying <sequence_file> using an argument
+.HP
+\fB\-\-dotter\-first\-match\fR
+.IP
+Call Dotter on the first match to the right of the default start coord.
+.HP
+\fB\-\-fetch\-server\fR <nodeid:port>
+.IP
+Causes Blixem to get sequences from a fetch server at machine 'nodeid' on the given
+port (default 22100).
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+More detailed usage information.
+.HP
+\fB\-\-hide\-big\-picture\fR
+.IP
+Hide the big picture section on start\-up.
+.HP
+\fB\-\-hide\-inactive\-strand\fR
+.IP
+Hide the inactive strand (i.e. the reverse strand, or the forward strand if the \fB\-R\fR option
+is used).
+.HP
+\fB\-\-highlight\-diffs\fR
+.IP
+Enable 'highlight differences' mode, where mismatches (rather than matches) are highlighted.
+.HP
+\fB\-\-invert\-sort\fR
+.IP
+Invert sorting order
+.HP
+\fB\-m\fR <from[:to]>, \fB\-\-map\-coords=\fR<from[:to]>
+.IP
+Map the coordinate system so that the given 'from' coordinate maps to the given
+\&'to' coordinate (or to '1' if 'to' is not given).
+.HP
+\fB\-n\fR, \fB\-\-negate\-coords\fR
+.IP
+When showing the reverse strand, negate the display coordinates.
+.HP
+\fB\-o\fR <n>, \fB\-\-offset=\fR<n>
+.IP
+Offset the reference sequence coordinate system by n.
+.HP
+\fB\-\-optional\-data\fR
+.IP
+Parse additional data such as organism and tissue\-type on start\-up.
+.HP
+\fB\-\-remove\-input\-files\fR
+.IP
+Delete the input files after they have been parsed.
+.HP
+\fB\-r\fR, \fB\-\-reverse\-strand\fR
+.IP
+Indicates that the given reference sequence is the reverse strand.
+.HP
+\fB\-\-save\-temp\-files\fR
+.IP
+Save any temporary files created by Blixem.
+.HP
+\fB\-\-show\-coverage\fR
+.IP
+Display the coverage section on start\-up.
+.HP
+\fB\-\-sort\-mode=\fR<mode>
+.IP
+Default sort mode. Use \fB\-\-help\fR option to see details.
+.HP
+\fB\-\-squash\-matches\fR
+.IP
+Compress the alignment lists on start\-up.
+.HP
+\fB\-s\fR <n>, \fB\-\-start\-coord=\fR<n>
+.IP
+Start with the display centred on coordinate n.
+.HP
+\fB\-\-start\-next\-match\fR
+.IP
+Start with the display centred on the first match to the right of the default start coord.
+.HP
+\fB\-y\fR <file>, \fB\-\-styles\-file=\fR<file>
+.IP
+Read color options from a key\-value file. Use \fB\-\-help\fR option to see details.
+.HP
+\fB\-\-version\fR
+.IP
+Show package version number.
+.HP
+\fB\-z\fR <start:end>, \fB\-\-zoom\-range=\fR<start:end>
+.IP
+Specify the initial range of coordinates to zoom the big picture in to.
+.HP
+\fB\-\-zoom\-whole\fR
+.IP
+Start with the big picture zoomed out to view the full reference sequence range.
+.IP
+Some X options:
+\fB\-acefont\fR <font> Main font.
+\fB\-font\fR    <font> Menu font.
+.PP
+\fB\-\-\-\-\-\fR
+.IP
+Written by Gemma Barson <gb10 at sanger.ac.uk>
+Based on original code by Erik Sonnhammer <Erik.Sonnhammer at sbc.su.se>
+.IP
+Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale
+.IP
+Sequence Homology Analysis. Comput. Applic. Biosci. 10:301\-307.
+.IP
+See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
+.IP
+Copyright (c) 2009\-2015: Genome Research Ltd.
+Blixem is distributed under the GNU Public License; see http://www.gnu.org/copyleft/gpl.txt
+.TP
+Version 4.44.1
+14:27:56 Oct 19 2017
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..3c802e4
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,40 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=belvu
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='View multiple alignments in good-looking colours' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=blixem
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='display multiple alignments against a reference sequence' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=blixemh
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='display multiple alignments against a reference sequence' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=dotter
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='Sequence dotplots with image enhancement tools' \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+
diff --git a/debian/dotter.1 b/debian/dotter.1
new file mode 100644
index 0000000..c83110f
--- /dev/null
+++ b/debian/dotter.1
@@ -0,0 +1,148 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH DOTTER "1" "October 2017" "dotter 4.44.1" "User Commands"
+.SH NAME
+dotter \- Sequence dotplots with image enhancement tools
+.SH DESCRIPTION
+.IP
+Dotter \- Sequence dotplots with image enhancement tools.
+.TP
+Usage: dotter [options] <horizontal_sequence> <vertical_sequence>
+[X options]
+.IP
+Where <horizontal_sequence> and <vertical_sequence> are file names for FASTA files
+containing the two sequences.
+.TP
+Allowed sequence types:
+Protein  \-   Protein
+DNA      \-   DNA
+DNA      \-   Protein
+.IP
+Options:
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Show this usage information
+.HP
+\fB\-b\fR <file>, \fB\-\-batch\-save=\fR<file>
+.IP
+Batch mode; save dot matrix to <file>
+.HP
+\fB\-e\fR <file>, \fB\-\-batch\-export=\fR<file>
+.IP
+Batch mode; export plot to PDF file <file>
+.HP
+\fB\-l\fR <file>, \fB\-\-load\fR
+.IP
+Load dot matrix from <file>
+.HP
+\fB\-m\fR <float>, \fB\-\-memory\-limit=\fR<float>
+.IP
+Memory usage limit in Mb (default 0.5)
+.HP
+\fB\-z\fR <int>, \fB\-\-zoom\fR
+.IP
+Set zoom (compression) factor
+.HP
+\fB\-p\fR <int>, \fB\-\-pixel\-factor\fR
+.IP
+Set pixel factor manually (ratio pixelvalue/score)
+.HP
+\fB\-W\fR <int>, \fB\-\-window\-size\fR
+.IP
+Set sliding window size. (K => Karlin/Altschul estimate)
+.HP
+\fB\-M\fR <file>, \fB\-\-matrix\-file=\fR<file>
+.IP
+Read in score matrix from <file> (Blast format; Default: Blosum62).
+.HP
+\fB\-F\fR <file>, \fB\-\-sequence\-file\fR
+.IP
+Read in sequences and data from <file> (replaces sequencefiles).
+.HP
+\fB\-f\fR <file>, \fB\-\-feature\-file\fR
+.IP
+Read feature segments from <file>
+.HP
+\fB\-H\fR, \fB\-\-hsp\-mode\fR
+.IP
+Do not calculate dotplot at startup.
+.HP
+\fB\-R\fR, \fB\-\-reverse\-greyramp\fR
+.IP
+Reversed Greyramp tool at start.
+.HP
+\fB\-r\fR, \fB\-\-reverse\-horizontal\fR
+.IP
+Reverse and complement horizontal_sequence (if DNA)
+.HP
+\fB\-v\fR, \fB\-\-reverse\-vertical\fR
+.IP
+Reverse and complement vertical_sequence (if DNA)
+.HP
+\fB\-D\fR, \fB\-\-disable\-mirror\fR
+.IP
+Don't display mirror image in self comparisons
+.HP
+\fB\-w\fR, \fB\-\-watson\-only\fR
+.IP
+For DNA: horizontal_sequence top strand only (Watson)
+.HP
+\fB\-c\fR, \fB\-\-crick\-only\fR
+.IP
+For DNA: horizontal_sequence bottom strand only (Crick)
+.HP
+\fB\-q\fR <int>, \fB\-\-horizontal\-offset=\fR<int>
+.IP
+Horizontal_sequence offset
+.HP
+\fB\-s\fR <int>, \fB\-\-vertical\-offset=\fR<int>
+.IP
+Vertical_sequence offset
+.HP
+\fB\-\-horizontal\-type\fR=\fI\,p\/\fR|d
+.IP
+Horizontal_sequence type ('p' for peptide or 'd' for DNA)
+.HP
+\fB\-\-vertical\-type\fR=\fI\,p\/\fR|d
+.IP
+Vertical_sequence type ('p' for peptide or 'd' for DNA)
+.HP
+\fB\-\-abbrev\-title\-on\fR
+.IP
+Abbreviate window title prefixes
+.HP
+\fB\-\-abbrev\-title\-off\fR
+.IP
+Do not abbreviate window title prefixes
+.HP
+\fB\-\-session_colour=\fR<colour_str>
+.IP
+Set the background colour of the dotter window
+.HP
+\fB\-\-compiled\fR
+.IP
+Show package compile date
+.HP
+\fB\-\-version\fR
+.IP
+Show package version
+.PP
+\fB\-\-\-\-\-\fR
+.IP
+Written by Gemma Barson <gb10 at sanger.ac.uk>
+Based on original code by Erik Sonnhammer <Erik.Sonnhammer at sbc.su.se>
+.IP
+Reference: Sonnhammer ELL & Durbin R (1995). A dot\-matrix program
+.IP
+with dynamic threshold control suited for genomic DNA and protein
+sequence analysis. Gene 167(2):GC1\-10.
+.IP
+See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
+.IP
+Copyright (c) 2010\-2015: Genome Research Ltd.
+Dotter is distributed under the GNU Public License; see http://www.gnu.org/copyleft/gpl.txt
+.TP
+Version 4.44.1
+14:27:56 Oct 19 2017
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/dotter.manpages b/debian/dotter.manpages
new file mode 100644
index 0000000..8b3e258
--- /dev/null
+++ b/debian/dotter.manpages
@@ -0,0 +1 @@
+debian/dotter.1

-- 
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