summarize-ancestors1

Construct alignments with internal sequences for labeled nodes in query tree.

Usage

summarize-ancestors alignment -A fastas1 -T trees1 [OPTIONS]

Construct alignments with internal sequences for labeled nodes in query tree.

`-h, –help`	produces help message
`-V, –verbose`	[=arg(=1)] Show more log messages on stderr.

`-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.

`-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.

Add ancestral sequences to summary alignment:

: % summarize-ancestors summary.fasta -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .

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

3 releases since Debian 11 (Bullseye); the text changed 1 time.