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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:

produces help message
[=arg(=1)] Show more log messages on stderr.

INPUT OPTIONS:

File of alignment samples
File of corresponding tree samples
factor by which to sub-sample trees

ANCESTOR QUERY OPTIONS:

Newick tree with labelled ancestors
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