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⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.