.\" 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.