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.TH "trees-consensus" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]trees-consensus\f[R] - Find consensus trees and supported splits.
.SH SYNOPSIS
.PP
\f[B]trees-consensus\f[R] [OPTIONS] \f[I]sampled-trees\f[R]
[\f[I]sampled-trees\f[R] \&...
\f[I]sampled-trees\f[R]]
.SH DESCRIPTION
.PP
Find consensus trees and supported splits.
.SH INPUT OPTIONS:
.TP
\f[B]-h\f[R], \f[B]\[en]help\f[R]
Produce help message.
.TP
\f[B]-V\f[R], \f[B]\[en]verbose\f[R]
Output more log messages on stderr.
.TP
\f[B]-s\f[R] \f[I]arg\f[R] (=10%), \f[B]\[en]skip\f[R] \f[I]arg\f[R] (=10%)
Number of trees to skip.
.TP
\f[B]-u\f[R] \f[I]arg\f[R], \f[B]\[en]until\f[R] \f[I]arg\f[R]
Read until this number of trees.
.TP
\f[B]-m\f[R] \f[I]arg\f[R], \f[B]\[en]max\f[R] \f[I]arg\f[R]
Thin tree samples down to this number of trees.
.TP
\f[B]-x\f[R] \f[I]arg\f[R] (=1), \f[B]\[en]subsample\f[R] \f[I]arg\f[R] (=1)
Factor by which to subsample.
.TP
\f[B]-i\f[R] \f[I]arg\f[R], \f[B]\[en]ignore\f[R] \f[I]arg\f[R]
Comma-separated list of taxa to ignore.
.SH REPORTING OPTIONS:
.TP
\f[B]\[en]map-trees\f[R] \f[I]arg\f[R] (=1)
Only report the top \f[I]arg\f[R] trees per file.
.TP
\f[B]\[en]min-support\f[R] \f[I]arg\f[R] (=0.25)
Minimum threshold PP for splits.
.TP
\f[B]\[en]report\f[R] \f[I]arg\f[R]
Write supported partitions to file \f[I]arg\f[R].
.TP
\f[B]\[en]map-tree\f[R] \f[I]arg\f[R]
Write out the map tree to file \f[I]arg\f[R].
.TP
\f[B]\[en]consensus\f[R] \f[I]arg\f[R]
Write out consensus trees.
.TP
\f[B]\[en]greedy-consensus\f[R] \f[I]arg\f[R]
Write out greedy consensus trees.
.TP
\f[B]\[en]extended-consensus-L\f[R] \f[I]arg\f[R]
Write out extended consensus trees + lengths.
.TP
\f[B]\[en]extended-consensus\f[R] \f[I]arg\f[R]
Write out extended consensus trees.
.TP
\f[B]\[en]support-levels\f[R] \f[I]arg\f[R]
Write #branches versus LOD to file \f[I]arg\f[R].
.TP
\f[B]\[en]extended-support-levels\f[R] \f[I]arg\f[R]
Write #sub-branches versus LOD to file \f[I]arg\f[R].
.SH SEARCH OPTIONS:
.TP
\f[B]\[en]sub-partitions\f[R]
Search for partial splits.
.TP
\f[B]\[en]depth\f[R] \f[I]arg\f[R] (=1)
Depth at which to look for partial splits.
.TP
\f[B]\[en]rooting\f[R] \f[I]arg\f[R] (=0.9)
Threshold in search for partial splits.
.TP
\f[B]\[en]odds-ratio\f[R] \f[I]arg\f[R] (=1.5)
Report partial-splits only if removing taxa improves the odds by at
least this ratio.
.SH EXAMPLES:
.PP
Compute the majority consensus tree, skipping the first 10% of trees:
.IP
.nf
\f[C]
% trees-consensus newick.trees > c50.tree
% trees-consensus newick.trees --skip=10% > c50.tree
\f[R]
.fi
.PP
Skip the first 100 trees:
.IP
.nf
\f[C]
% trees-consensus newick.trees --skip=100 > c50.tree
\f[R]
.fi
.PP
Skip the first 20% of trees and take every 10th tree thereafter:
.IP
.nf
\f[C]
% trees-consensus newick.trees --skip=20% -x10 > c50.tree
\f[R]
.fi
.PP
Compute the 50% (majority) and 80% consensus trees:
.IP
.nf
\f[C]
% trees-consensus newick.trees --consensus=0.5:c50.tree,0.8:c80.tree
% trees-consensus newick.trees --consensus=0.5,0.8:c80.tree > c50.tree
\f[R]
.fi
.PP
Compute the MAP tree and write a summary of supported partitions:
.IP
.nf
\f[C]
% trees-consensus --map-tree=MAP.tree --report=partitions.txt
\f[R]
.fi
.PP
Compute the MAP tree and write it to the standard output:
.IP
.nf
\f[C]
% trees-consensus --map-tree=- --report=partitions.txt
\f[R]
.fi
.SH REPORTING BUGS:
.PP
BAli-Phy online help: <http://www.bali-phy.org/docs.php>.
.PP
Please send bug reports to <bali-phy-users@googlegroups.com>.
.SH AUTHORS
Benjamin Redelings.