NAME¶

SYNOPSIS¶

DESCRIPTION¶

GENERAL OPTIONS:¶

-h, --help

produce help message

INPUT OPTIONS:¶

--alphabet arg

set to 'Codons' to prefer codon alphabets

OUTPUT OPTIONS:¶

--merge

Stack the two alignments into one alignment with duplicate names

--dual

Write out the two aligned alignments separately

--fill arg (=gap)

blank columns filled with: gap or unknown

-d arg, --differences-file arg

Filename to store differences in AU format

REPORTING BUGS:¶

Please send bug reports to <bali-phy-users@googlegroups.com>.

AUTHORS¶