bionic (1) timetree_inference.1.gz

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.