Man page - alignment-gild(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
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Documentations in package:
Manual
| alignment-gild(1) | alignment-gild(1) |
NAME
alignment-gild - Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.
SYNOPSIS
alignment-gild alignment-file tree-file alignments-file [alignments-file] [OPTIONS]
DESCRIPTION
Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.
ALLOWED OPTIONS:
- -h, –help
- produce help message
- –align arg
- file with alignment to annotate
- –tree arg
- file with tree
- –find-root
- estimate the root position from branch lengths
- –alphabet arg
- set to `Codons' to prefer codon alphabets
- –skip arg (=0)
- number of alignment samples to skip
- –max-alignments arg (=1000)
- maximum number of alignments to analyze
- -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 |