Man page - summarize-ancestors(1)

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Package: bali-phy
apt-get install bali-phy

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

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

Benjamin Redelings.