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.