[med-svn] [python-treetime] 04/06: Add manpages

Thu Jun 15 12:08:49 UTC 2017

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tille pushed a commit to branch master
in repository python-treetime.

commit 8d6e4e503e06bf4bbe66aba2eaa2e6921e38c890
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 15 09:45:38 2017 +0200

    Add manpages
---
 debian/manpages                        |  1 +
 debian/mans/ancestral_reconstruction.1 | 37 +++++++++++++++++++
 debian/mans/temporal_signal.1          | 39 ++++++++++++++++++++
 debian/mans/timetree_inference.1       | 65 ++++++++++++++++++++++++++++++++++
 4 files changed, 142 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/ancestral_reconstruction.1 b/debian/mans/ancestral_reconstruction.1
new file mode 100644
index 0000000..a78db4d
--- /dev/null
+++ b/debian/mans/ancestral_reconstruction.1
@@ -0,0 +1,37 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH ANCESTRAL_RECONSTRUCTION "1" "June 2017" "ancestral_reconstruction 0.0+20170607" "User Commands"
+.SH NAME
+ancestral_reconstruction \- Reconstructs ancestral sequences and maps mutations to the tree
+.SH SYNOPSIS
+.B ancestral_reconstruction
+[\-h] \fB\-\-aln\fR ALN \fB\-\-tree\fR TREE [\-\-prot] [\-\-marginal] [\-\-infer_gtr] [\-\-keep_overhangs]
+.PP
+.SH DESCRIPTION
+Reconstructs ancestral sequences and maps mutations to the tree. The output
+consists of a file ending with _ancestral.fasta with ancestral sequences and a
+tree ending with _mutation.nexus with mutations added as comments like
+_A45G_... The inferred GTR model is written to stdout
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-aln\fR ALN
+fasta file with input sequences
+.TP
+\fB\-\-tree\fR TREE
+newick file with tree
+.TP
+\fB\-\-prot\fR
+protein alignment
+.TP
+\fB\-\-marginal\fR
+marginal instead of joint ML reconstruction
+.TP
+\fB\-\-infer_gtr\fR
+infer substitution model
+.TP
+\fB\-\-keep_overhangs\fR
+do not fill terminal gaps
+.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/mans/temporal_signal.1 b/debian/mans/temporal_signal.1
new file mode 100644
index 0000000..ae6d710
--- /dev/null
+++ b/debian/mans/temporal_signal.1
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH TEMPORAL_SIGNAL "1" "June 2017" "temporal_signal 0.0+20170607" "User Commands"
+.SH NAME
+temporal_signal \- Calculates the root-to-tip regression and quantifies the 'clock-i-ness' of a tree
+.SH SYNOPSIS
+.B temporal_signal
+[\-h] \fB\-\-tree\fR TREE \fB\-\-dates\fR DATES [\-\-aln ALN] [\-\-infer_gtr] [\-\-reroot] [\-\-plot] [\-\-verbose VERBOSE]
+.PP
+.SH DESCRIPTION
+Calculates the root\-to\-tip regression and quantifies the 'clock\-i\-ness' of the
+tree. It will optionally reroot the tree to maximize the clock\-like signal and
+recalculate branch length.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-tree\fR TREE
+newick file with tree
+.TP
+\fB\-\-dates\fR DATES
+csv with dates for nodes with 'node_name, date' where
+date is float (as in 2012.15)
+.TP
+\fB\-\-aln\fR ALN
+fasta file with input sequences
+.TP
+\fB\-\-infer_gtr\fR
+infer substitution model
+.TP
+\fB\-\-reroot\fR
+reroot the tree to maximize the correlation of root\-totip distance with sampling time
+.HP
+\fB\-\-plot\fR
+.TP
+\fB\-\-verbose\fR VERBOSE
+verbosity of output 0\-6
+.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/mans/timetree_inference.1 b/debian/mans/timetree_inference.1
new file mode 100644
index 0000000..ba2de05
--- /dev/null
+++ b/debian/mans/timetree_inference.1
@@ -0,0 +1,65 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH TIMETREE_INFERENCE "1" "June 2017" "timetree_inference 0.0+20170607" "User Commands"
+.SH NAME
+timetree_inference \- Reconstructs ancestral sequences and infers a molecular clock tree
+.SH SYNOPSIS
+.B timetree_inference
+[\-h] \fB\-\-aln\fR ALN \fB\-\-tree\fR TREE \fB\-\-dates\fR DATES
+[\-\-infer_gtr] [\-\-reroot REROOT]
+[\-\-resolve_polytomies] [\-\-relax [RELAX [RELAX ...]]]
+[\-\-max_iter MAX_ITER] [\-\-verbose VERBOSE] [\-\-Tc TC]
+[\-\-plot]
+.PP
+.SH DESCRIPTION
+Reconstructs ancestral sequences and infers a molecular clock tree. The output
+consists of a file ending with _ancestral.fasta with ancestral sequences and a
+tree ending with _mutation.newick with mutations appended to node names as
+_A45G_.... The branches of this tree are scaled such that branch length
+correspond to times in units of the molecular clock. The molecular clock,
+along with the inferred GTR model, is written to stdout
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-aln\fR ALN
+fasta file with input sequences
+.TP
+\fB\-\-tree\fR TREE
+newick file with tree
+.TP
+\fB\-\-dates\fR DATES
+csv with dates for nodes with 'node_name, date' where
+date is float (as in 2012.15)
+.TP
+\fB\-\-infer_gtr\fR
+infer substitution model
+.TP
+\fB\-\-reroot\fR REROOT
+reroot the tree. Valid arguments are 'best',
+\&'midpoint', or a node name
+.TP
+\fB\-\-resolve_polytomies\fR
+resolve polytomies using temporal information.
+.TP
+\fB\-\-relax\fR [RELAX [RELAX ...]]
+use an autocorrelated molecular clock. Prior strength
+and coupling of parent and offspring rates can be
+specified e.g. as \fB\-\-relax\fR 1.0 0.5
+.TP
+\fB\-\-max_iter\fR MAX_ITER
+maximal number of iterations the inference cycle is
+run
+.TP
+\fB\-\-verbose\fR VERBOSE
+verbosity of output 0\-6
+.TP
+\fB\-\-Tc\fR TC
+coalescent time scale \fB\-\-\fR sensible values are on the
+order of the average hamming distance of
+contemporaneous sequences
+.TP
+\fB\-\-plot\fR
+plot the tree on a time axis
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

-- 
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