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alignment-gild(1) alignment-gild(1)

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:

produce help message
file with sequences and initial alignment
file with initial tree
estimate the root position from branch lengths
set to 'Codons' to prefer codon alphabets
number of alignment samples to skip
maximum number of alignments to analyze
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.

Feb 2018