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.

AUTHORS

Benjamin Redelings.