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.

                                                    Feb 2018                              alignment-consensus(1)