Man page - summarize-ancestors(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
| summarize-ancestors(1) | summarize-ancestors(1) |
NAME
summarize-ancestors - Construct alignments with internal sequences for labeled nodes in query tree.
SYNOPSIS
summarize-ancestors alignment -A fastas1 -T trees1 [OPTIONS]
DESCRIPTION
Construct alignments with internal sequences for labeled nodes in query tree.
GENERAL OPTIONS:
- -h, –help
- produces help message
- -V, –verbose
- [=arg(=1)] Show more log messages on stderr.
INPUT OPTIONS:
- -A arg, –alignments arg
- File of alignment samples
- -T arg, –trees arg
- File of corresponding tree samples
- -x arg (=10), –subsample arg (=10)
- factor by which to sub-sample trees
- -m arg (=500), –max arg (=500)
- Thin (alignment,tree) pairs down to this number of samples.
ANCESTOR QUERY OPTIONS:
- -n arg, –nodes arg
- Newick tree with labelled ancestors
- -g arg, –groups arg
- File with named groups
- –nodes-min arg (=0.34)
- Minimum fraction to include a node.
- –groups-min arg (=0.34)
- Minimum fraction to include a group.
EXAMPLES:
Add ancestral sequences to summary alignment:
-
% summarize-ancestors summary.fasta -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree
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 |