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

SEE ALSO

       https://github.com/neherlab/treetime

EXAMPLES

       https://github.com/neherlab/treetime_examples

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.