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.