NAME

       alignment-gild  - Annotate each residue in the alignment according to the probability that
       it should align to the hypothetical root character in its column.

SYNOPSIS

       alignment-gild alignment-file tree-file ...  [OPTIONS] < alignments-file

DESCRIPTION

       Annotate each residue in the alignment according to the probability that it  should  align
       to the hypothetical root character in its column.

ALLOWED OPTIONS:

       -h, --help
              produce help message

       --align arg
              file with sequences and initial alignment

       --tree arg
              file with initial tree

       --find-root
              estimate the root position from branch lengths

       --alphabet arg
              set to 'Codons' to prefer codon alphabets

       --skip arg (=0)
              number of alignment samples to skip

       --max-alignments arg (=1000)
              maximum number of alignments to analyze

       -V, --verbose
              Output more log messages on stderr.

REPORTING BUGS:

       BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

       Please send bug reports to <bali-phy-users@googlegroups.com>.

AUTHORS

       Benjamin Redelings.

                                             Feb 2018                           alignment-gild(1)