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.TH "trees\-consensus" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]trees\-consensus\f[] \- Find consensus trees and supported splits.
.SH SYNOPSIS
.PP
\f[B]trees\-consensus\f[] [OPTIONS] \f[I]sampled\-trees\f[]
[\f[I]sampled\-trees\f[] ...
\f[I]sampled\-trees\f[]]
.SH DESCRIPTION
.PP
Find consensus trees and supported splits.
.SH INPUT OPTIONS:
.TP
.B \f[B]\-h\f[], \f[B]\-\-help\f[]
Produce help message.
.RS
.RE
.TP
.B \f[B]\-s\f[] \f[I]arg\f[] (=10%), \f[B]\-\-skip\f[] \f[I]arg\f[] (=10%)
Number of trees to skip.
.RS
.RE
.TP
.B \f[B]\-u\f[] \f[I]arg\f[], \f[B]\-\-until\f[] \f[I]arg\f[]
Read until this number of trees.
.RS
.RE
.TP
.B \f[B]\-m\f[] \f[I]arg\f[], \f[B]\-\-max\f[] \f[I]arg\f[]
Thin tree samples down to this number of trees.
.RS
.RE
.TP
.B \f[B]\-x\f[] \f[I]arg\f[] (=1), \f[B]\-\-subsample\f[] \f[I]arg\f[] (=1)
Factor by which to subsample.
.RS
.RE
.TP
.B \f[B]\-\-ignore\f[] \f[I]arg\f[]
Comma\-separated list of taxa to ignore.
.RS
.RE
.SH REPORTING OPTIONS:
.TP
.B \f[B]\-\-map\-trees\f[] \f[I]arg\f[] (=1)
Only report the top trees per file.
.RS
.RE
.TP
.B \f[B]\-\-map\-tree\f[] \f[I]arg\f[]
Write out the map tree to file .
.RS
.RE
.TP
.B \f[B]\-\-min\-support\f[] \f[I]arg\f[] (=0.25)
Minimum threshold PP for splits.
.RS
.RE
.TP
.B \f[B]\-\-report\f[] \f[I]arg\f[]
Write supported partitions to file .
.RS
.RE
.TP
.B \f[B]\-\-consensus\-PP\f[] \f[I]arg\f[]
Write out consensus trees+PP.
.RS
.RE
.TP
.B \f[B]\-\-consensus\f[] \f[I]arg\f[]
Write out consensus trees.
.RS
.RE
.TP
.B \f[B]\-\-greedy\-consensus\f[] \f[I]arg\f[]
Write out greedy consensus trees.
.RS
.RE
.TP
.B \f[B]\-\-extended\-consensus\-L\f[] \f[I]arg\f[]
Write out extended consensus trees + lengths.
.RS
.RE
.TP
.B \f[B]\-\-extended\-consensus\f[] \f[I]arg\f[]
Write out extended consensus trees.
.RS
.RE
.TP
.B \f[B]\-\-support\-levels\f[] \f[I]arg\f[]
Write #branches versus LOD to file .
.RS
.RE
.TP
.B \f[B]\-\-extended\-support\-levels\f[] \f[I]arg\f[]
Write #sub\-branches versus LOD to file .
.RS
.RE
.TP
.B \f[B]\-\-odds\-ratio\f[] \f[I]arg\f[] (=1.5)
Report partial\-splits only if removing taxa improves the odds by at
least this ratio.
.RS
.RE
.TP
.B \f[B]\-v\f[], \f[B]\-\-verbose\f[]
Output more log messages on stderr.
.RS
.RE
.SH SEARCH OPTIONS:
.TP
.B \f[B]\-\-sub\-partitions\f[]
Search for partial splits.
.RS
.RE
.TP
.B \f[B]\-\-depth\f[] \f[I]arg\f[] (=1)
Depth at which to look for partial splits.
.RS
.RE
.TP
.B \f[B]\-\-rooting\f[] \f[I]arg\f[] (=0.9)
Threshold in search for partial splits.
.RS
.RE
.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.