NAME

       alignment-max - Construct a posterior decoding alignment to summarize an alignment sample.

SYNOPSIS

       alignment-max [OPTIONS] < alignments-file

DESCRIPTION

       Construct a posterior decoding 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-alignments arg (=1000)
              Maximum number of alignments to analyze

       –analysis arg (=multiply)
              sum, wsum, wsum2, multiply

       –column-pr arg (=homology)
              homology, alignment

       -S arg (=1), –sort arg (=1)
              Sort partially ordered columns to group similar gaps

       -o arg (=-), –out arg (=-)
              Output file (defaults to stdout)

       -p arg, –out-probabilities arg
              Output file for column probabilities, if specified

       –debug-graph arg
              Filename for debug graph

       -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-max(1)