Man page - alignment-max(1)
Packages contas this manual
- alignment-distances(1)
- alignment-max(1)
- bali-phy(1)
- tree-mean-lengths(1)
- mcon-tool(1)
- extract-ancestors(1)
- cut-range(1)
- alignment-indices(1)
- alignment-thin(1)
- stats-select(1)
- pickout(1)
- trees-consensus(1)
- alignment-gild(1)
- alignment-chop-internal(1)
- summarize-ancestors(1)
- draw-tree(1)
- bali-phy-pkg(1)
- mctree-mean-lengths(1)
- tree-tool(1)
- alignment-find(1)
- trees-bootstrap(1)
- alignment-translate(1)
- trees-distances(1)
- alignment-cat(1)
- statreport(1)
- bp-analyze(1)
- alignment-info(1)
- alignment-draw(1)
- alignments-diff(1)
- alignment-consensus(1)
- bali-subsample(1)
Package: bali-phy
apt-get install bali-phy
apt-get install bali-phy
Manuals in package:
Documentations in package:
Manual
| alignment-max(1) | alignment-max(1) |
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 |