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 hypothet‐
       ical 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)