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       timetree_inference - Reconstructs ancestral sequences and infers a molecular clock tree


       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]


       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


       -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 substitution model

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

              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


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