Man page - alignment-indices(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-indices(1) | alignment-indices(1) |
NAME
alignment-indices - Show the alignment in terms of the index of each character in its sequence.
SYNOPSIS
alignment-indices alignment-file [OPTIONS]
DESCRIPTION
Show the alignment in terms of the index of each character in its sequence.
ALLOWED OPTIONS:
- -h, –help
- produce help message
- –align arg
- file with sequences and initial alignment
- –alphabet arg
- set to `Codons' to prefer codon alphabets
- -c arg, –columns arg
- Ranges of columns to keep, like: 1-10,30-
- –invariant arg
- print only sites where this site and arg neighbors are invariant.
- –differences arg
- how many sequences may differ from the majority?
- –avoid-gaps arg (=3)
- How far from a gap must a column be to be invariant?
- –min-constraints arg
- Minimum # of constraints per column for a constraint to be emitted
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 |