.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH TREETIME "1" "September 2018" "treetime 0.5.0" "User Commands"
.SH NAME
treetime \- Maximum Likelihood Phylodynamics
.SH SYNOPSIS
.B treetime
<positional> [optional]
.SH DESCRIPTION
TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.
.P
To optimize the likelihood of time-scaled phylogenies, TreeTime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstrained nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool on the command-line or as a library used in larger phylogenetic analysis work-flows.
.SH OPTIONS
.SS positional arguments
.TP
\fBancestral\fR
infer ancestral sequences maximizing the joint or marginal likelihood.
.TP
\fBhomoplasy\fR
analyze patterns of recurrent mutations aka homoplasies.
.TP
\fBclock\fR
estimate molecular clock parameters and reroot the tree.
.TP
\fBmugration\fR
map discrete character such as host or country to the tree.
.SS optional arguments
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-tree\fR TREE
Name of file containing the tree in newick, nexus, or
phylip format. If none is provided, treetime will
attempt to build a tree from the alignment using
fasttree, iqtree, or raxml (assuming they are
installed)
.TP
\fB\-\-sequence\-length\fR SEQUENCE_LENGTH
length of the sequence, used to calculate expected
variation in branch length. Not required if alignment
is provided.
.TP
\fB\-\-aln\fR ALN
alignment file (fasta)
.TP
\fB\-\-vcf\-reference\fR VCF_REFERENCE
only for vcf input: fasta file of the sequence the VCF
was mapped to.
.TP
\fB\-\-dates\fR DATES
csv file with dates for nodes with 'node_name, date'
where date is float (as in 2012.15)
.TP
\fB\-\-clock\-filter\fR CLOCK_FILTER
ignore tips that don't follow a loose clock, 'clockfilter=number of interquartile ranges from regression'
.TP
\fB\-\-reroot\fR REROOT
reroot the tree. Valid choices are 'ML', 'ML\-rough',
\&'least\-squares', 'min_dev', 'midpoint' or a node name
to be used as outgroup. Use \fB\-\-keep\-root\fR to keep the
current root.
.TP
\fB\-\-keep\-root\fR
don't reroot the tree. Otherwise, reroot to minimize
the the residual of the regression of root\-to\-tip
distance and sampling time
.TP
\fB\-\-gtr\fR GTR
GTR model to use. '\-\-gtr infer' will infer a model
from the data. Alternatively, specify the model type.
If the specified model requires additional options,
use '\-\-gtr\-params' to specify those.
.TP
\fB\-\-gtr\-params\fR GTR_PARAMS [GTR_PARAMS ...]
GTR parameters for the model specified by the \fB\-\-gtr\fR
argument. The parameters should be feed as 'key=value'
list of parameters. Example: '\-\-gtr K80 \fB\-\-gtr\-params\fR
kappa=0.2 pis=0.25,0.25,0.25,0.25'. See the exact
definitions of the parameters in the GTR creation
methods in treetime/nuc_models.py or
treetime/aa_models.py
.TP
\fB\-\-clock\-rate\fR CLOCK_RATE
if specified, the rate of the molecular clock won't be
optimized.
.TP
\fB\-\-branch\-length\-mode\fR {auto,input,joint,marginal}
If set to 'input', the provided branch length will be
used without modification. Note that branch lengths
optimized by treetime are only accurate at short
evolutionary distances.
.TP
\fB\-\-confidence\fR
estimate confidence intervals of divergence times.
.TP
\fB\-\-keep\-polytomies\fR
Don't 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. Note that for polytomy resolution and coalescence
models max_iter should be at least 2
.TP
\fB\-\-coalescent\fR COALESCENT
coalescent time scale \fB\-\-\fR sensible values are on the
order of the average hamming distance of
contemporaneous sequences. In addition, 'opt'
\&'skyline' are valid options and estimate a constant
coalescent rate or a piecewise linear coalescent rate
history
.TP
\fB\-\-plot\-tree\fR PLOT_TREE
filename to save the plot to. Suffix will determine
format (choices pdf, png, svg, default=pdf)
.TP
\fB\-\-plot\-rtt\fR PLOT_RTT
filename to save the plot to. Suffix will determine
format (choices pdf, png, svg, default=pdf)
.TP
\fB\-\-keep\-overhangs\fR
do not fill terminal gaps
.TP
\fB\-\-zero\-based\fR
zero based mutation indexing
.TP
\fB\-\-report\-ambiguous\fR
include transitions involving ambiguous states
.TP
\fB\-\-verbose\fR VERBOSE
verbosity of output 0\-6
.TP
\fB\-\-outdir\fR OUTDIR
directory to write the output to
.SH SEE ALSO
https://github.com/neherlab/treetime
.SH EXAMPLES
https://github.com/neherlab/treetime_examples
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.