NAME

       timetree_inference - Reconstructs ancestral sequences and infers a molecular clock tree

SYNOPSIS

       timetree_inference   [-h]   --aln   ALN   --tree  TREE  --dates  DATES  [--infer_gtr]  [--reroot  REROOT]
       [--resolve_polytomies] [--relax [RELAX [RELAX ...]]]  [--max_iter MAX_ITER] [--verbose VERBOSE] [--Tc TC]
       [--plot]

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

OPTIONS

       -h, --help
              show this help message and exit

       --aln ALN
              fasta file with input sequences

       --tree TREE
              newick file with tree

       --dates DATES
              csv with dates for nodes with 'node_name, date' where date is float (as in 2012.15)

       --infer_gtr
              infer substitution model

       --reroot REROOT
              reroot the tree. Valid arguments are 'best', 'midpoint', or a node name

       --resolve_polytomies
              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

       --verbose VERBOSE
              verbosity of output 0-6

       --Tc TC
              coalescent  time  scale  --  sensible  values  are on the order of the average hamming distance of
              contemporaneous sequences

       --plot plot the tree on a time axis

AUTHOR

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

timetree_inference 0.0+20170607                     June 2017                              TIMETREE_INFERENCE(1)