NAME¶
treetime - Maximum Likelihood Phylodynamics
SYNOPSIS¶
treetime <positional> [optional]
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.
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.
OPTIONS¶
positional arguments¶
- ancestral
- infer ancestral sequences maximizing the joint or marginal
likelihood.
- homoplasy
- analyze patterns of recurrent mutations aka homoplasies.
- clock
- estimate molecular clock parameters and reroot the tree.
- mugration
- map discrete character such as host or country to the tree.
optional arguments¶
- -h, --help
- show this help message and exit
- --tree 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)
- --sequence-length SEQUENCE_LENGTH
- length of the sequence, used to calculate expected variation in branch
length. Not required if alignment is provided.
- --aln ALN
- alignment file (fasta)
- --vcf-reference VCF_REFERENCE
- only for vcf input: fasta file of the sequence the VCF was mapped to.
- --dates DATES
- csv file with dates for nodes with 'node_name, date' where date is float
(as in 2012.15)
- --clock-filter CLOCK_FILTER
- ignore tips that don't follow a loose clock, 'clockfilter=number of
interquartile ranges from regression'
- --reroot 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
--keep-root to keep the current root.
- --keep-root
- don't reroot the tree. Otherwise, reroot to minimize the the residual of
the regression of root-to-tip distance and sampling time
- --gtr 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.
- --gtr-params GTR_PARAMS [GTR_PARAMS ...]
- GTR parameters for the model specified by the --gtr argument. The
parameters should be feed as 'key=value' list of parameters. Example:
'--gtr K80 --gtr-params 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
- --clock-rate CLOCK_RATE
- if specified, the rate of the molecular clock won't be optimized.
- --branch-length-mode {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.
- --confidence
- estimate confidence intervals of divergence times.
- --keep-polytomies
- Don't resolve polytomies using temporal information.
- --relax [RELAX [RELAX ...]]
- use an autocorrelated molecular clock. Prior strength and coupling of
parent and offspring rates can be specified e.g. as --relax 1.0
0.5
- --max-iter 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
- --coalescent COALESCENT
- coalescent time scale -- 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
- --plot-tree PLOT_TREE
- filename to save the plot to. Suffix will determine format (choices pdf,
png, svg, default=pdf)
- --plot-rtt PLOT_RTT
- filename to save the plot to. Suffix will determine format (choices pdf,
png, svg, default=pdf)
- --keep-overhangs
- do not fill terminal gaps
- --zero-based
- zero based mutation indexing
- --report-ambiguous
- include transitions involving ambiguous states
- --verbose VERBOSE
- verbosity of output 0-6
- --outdir OUTDIR
- directory to write the output to
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.
