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.