alignment-max - Construct a posterior decoding alignment to
summarize an alignment sample.
alignment-max [OPTIONS] < alignments-file
Construct a posterior decoding alignment to summarize an alignment
sample.
- -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.