NAME

alignment-compare - Compare two alignment distributions.

SYNOPSIS

alignment-compare alignment-file1 alignment-file2 [OPTIONS]

DESCRIPTION

Compare two alignment distributions.

ALLOWED OPTIONS:

-h, --help

produce help message

--alphabet arg

Specify the alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop.

--seed arg

random seed

--align arg

alignment to output values for.

--max-alignments arg (=1000)

maximum number of alignments to analyze

--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.