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 alignments-file [alignments-file] [OPTIONS]

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 alignment to annotate

       –tree arg
              file with 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)