alignment−gild

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 AT googlegroups DOT com>.

AUTHORS

Benjamin Redelings.