alignment-gild - Annotate each residue in the alignment according to the probability that it should align

-h, –help
              produce help message

       –alignarg
              file with sequences and initial alignment

       –treearg
              file with initial tree

       –find-root
              estimate the root position from branch lengths

       –alphabetarg
              set to `Codons' to prefer codon alphabets

       –skiparg (=0)
              number of alignment samples to skip

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

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

       Benjamin Redelings.

                                                    Feb 2018                                   alignment-gild(1)

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

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

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

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

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