NAME

       ancestral_reconstruction - Reconstructs ancestral sequences and maps mutations to the tree

SYNOPSIS

       ancestral_reconstruction    [-h]    --aln   ALN   --tree   TREE   [--prot]   [--marginal]   [--infer_gtr]
       [--keep_overhangs]

DESCRIPTION

       Reconstructs ancestral sequences and maps mutations to the tree. The output consists  of  a  file  ending
       with  _ancestral.fasta  with  ancestral  sequences  and a tree ending with _mutation.nexus with mutations
       added as comments like _A45G_... 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

       --prot protein alignment

       --marginal
              marginal instead of joint ML reconstruction

       --infer_gtr
              infer substitution model

       --keep_overhangs
              do not fill terminal gaps

AUTHOR

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

ancestral_reconstruction 0.0+20170607               June 2017                        ANCESTRAL_RECONSTRUCTION(1)