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 alignments-file [alignments-file] [OPTIONS]

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 alignment to annotate

–tree arg

file with 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.