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commit 9e7572784c50a347593c0d1b0d5b4ab10381dd65 Author: Andreas Tille <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/alter-sequence-alignment.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
