treetime - Maximum Likelihood Phylodynamics

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

treetime 0.5.0                                   September 2018                                      TREETIME(1)

       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.

       https://github.com/neherlab/treetime_examples

       treetime - Maximum Likelihood Phylodynamics

positionalargumentsancestral
              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.

   optionalarguments-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

       https://github.com/neherlab/treetime

treetime <positional> [optional]