NAME

alignment-consensus - Construct a consensus alignment to summarize an alignment sample.

SYNOPSIS

alignment-consensus alignments-file [alignments-file ...] [OPTIONS]

DESCRIPTION

Construct a consensus alignment to summarize an alignment sample.

ALLOWED OPTIONS:

-h, --help

produce help message

--alphabet arg

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

-s arg (=0), --skip arg (=0)

number of alignment samples to skip

-m arg (=1000), --max arg (=1000)

maximum number of alignments to analyze

--strict arg

ignore events below this probability

--cutoff arg

ignore events below this probability

--uncertainty arg

file-name for AU uncertainty vs level

--chop-to arg

keep only the first arg taxa

-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.