alignments-diff

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

--blocksize arg (=20)

Width of blocks of same color

--classes arg (=1)

Number of groups for non-matching characters

REPORTING BUGS:

AUTHORS