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.