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⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.