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                              summarize-ancestors(1)