[med-svn] [alter-sequence-alignment] 04/08: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository alter-sequence-alignment.

commit 9e7572784c50a347593c0d1b0d5b4ab10381dd65
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 5 18:56:29 2015 +0200

    Add manpage
---
 debian/alter-sequence-alignment.1 | 66 +++++++++++++++++++++++++++++++++++++++
 debian/manpages                   |  1 +
 2 files changed, 67 insertions(+)

diff --git a/debian/alter-sequence-alignment.1 b/debian/alter-sequence-alignment.1
new file mode 100644
index 0000000..0f71380
--- /dev/null
+++ b/debian/alter-sequence-alignment.1
@@ -0,0 +1,66 @@
+.TH ALTER-SEQUENCE-ALIGNMENT "1" "September 2015" "alter-sequence-alignment 1.3.3" "User Commands"
+.SH NAME
+alter-sequence-alignment \- genomic sequences ALignment Transformation EnviRonment
+.SH SYNOPSIS
+.B alter-sequence-alignment
+\fI[option] [sequence]\fR
+.SH DESCRIPTION
+ ALTER (ALignment Transformation EnviRonment) is a tool to transform
+ between multiple sequence alignment formats. ALTER focuses on the
+ specifications of mainstream alignment and analysis programs rather than
+ on the conversion among more or less specific formats.
+.SH OPTIONS
+.TP
+\fB\-c\fR (\fB\-\-collapse\fR)
+Collapse sequences to haplotypes.
+.TP
+\fB\-cg\fR (\fB\-\-collapseGaps\fR)
+Treat gaps as missing data when collapsing.
+.TP
+\fB\-cl\fR (\fB\-\-collapseLimit\fR) N
+Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0).
+.TP
+\fB\-cm\fR (\fB\-\-collapseMissing\fR)
+Count missing data as differences when collapsing.
+.TP
+\fB\-i\fR (\fB\-\-input\fR) FILE
+Input file.
+.TP
+\fB\-ia\fR (\fB\-\-inputAutodetect\fR)
+Autodetect format (other input options are omitted).
+.TP
+\fB\-if\fR (\fB\-\-inputFormat\fR) VAL
+Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR).
+.TP
+\fB\-io\fR (\fB\-\-inputOS\fR) VAL
+Input operating system (Linux, MacOS or Windows)
+.TP
+\fB\-ip\fR (\fB\-\-inputProgram\fR) VAL
+Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee).
+.TP
+\fB\-o\fR (\fB\-\-output\fR) FILE
+Output file.
+.TP
+\fB\-of\fR (\fB\-\-outputFormat\fR) VAL
+Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR).
+.TP
+\fB\-ol\fR (\fB\-\-outputLowerCase\fR)
+Lowe case output.
+.TP
+\fB\-om\fR (\fB\-\-outputMatch\fR)
+Output match characters.
+.TP
+\fB\-on\fR (\fB\-\-outputResidueNumbers\fR)
+Output residue numbers (only ALN format).
+.TP
+\fB\-oo\fR (\fB\-\-outputOS\fR) VAL
+Output operating system (Linux, MacOS or Windows).
+.TP
+\fB\-op\fR (\fB\-\-outputProgram\fR) VAL
+Output program (jModelTest, MrBayes, PAML, PAUP,
+PhyML, ProtTest, RAxML, TCS, CodABC, BioEdit, MEGA,
+dnaSP, Se\-Al, Mesquite, SplitsTree, Clustal
+, MAFFT, MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)
+.TP
+\fB\-os\fR (\fB\-\-outputSequential\fR)
+Sequential output (only NEXUS and PHYLIP formats).
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

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