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.TH "trees\-distances" "1" "Feb 2018" "" ""
.hy
.SH NAME
.PP
\f[B]trees\-distances\f[] \- Compute autocorrelations or other functions
of tree distances.
.SH SYNOPSIS
.PP
\f[B]trees\-distances\f[] \f[I]analysis\f[] trees\-file1 [trees\-file2
\&...]
.SH DESCRIPTION
.PP
Compute autocorrelations or other functions of tree distances.
.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[] (=0), \f[B]\-\-skip\f[] \f[I]arg\f[] (=0)
number of tree samples 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]\-v\f[], \f[B]\-\-verbose\f[]
Output more log messages on stderr.
.RS
.RE
.SH ANALYSIS OPTIONS:
.TP
.B \f[B]\-\-analysis\f[] \f[I]arg\f[] (=matrix)
Analysis: matrix, autocorrelation, diameter, compare, convergence,
converged.
.RS
.RE
.TP
.B \f[B]\-\-metric\f[] \f[I]arg\f[] (=topology)
Tree distance: topology, branch, internal\-branch.
.RS
.RE
.TP
.B \f[B]\-\-remove\-duplicates\f[]
[matrix]: disallow zero distances between points.
.RS
.RE
.TP
.B \f[B]\-\-max\-lag\f[] \f[I]arg\f[]
[autocorrelation]: max lag to consider.
.RS
.RE
.TP
.B \f[B]\-\-CI\f[] \f[I]arg\f[] (=0.95)
Confidence interval size.
.RS
.RE
.TP
.B \f[B]\-\-converged\f[] \f[I]arg\f[] (=0.05)
Comma\-separated quantiles of distance required for converged?
(smaller is more strict).
.RS
.RE
.TP
.B \f[B]\-\-mean\f[]
Show mean and standard deviation
.RS
.RE
.TP
.B \f[B]\-\-median\f[]
Show median and confidence interval
.RS
.RE
.TP
.B \f[B]\-\-minmax\f[]
Show minimum and maximum distances
.RS
.RE
.TP
.B \f[B]\-\-leaves\-only\f[]
Show minimum and maximum distances
.RS
.RE
.TP
.B \f[B]\-\-topology\-only\f[]
Show minimum and maximum distances
.RS
.RE
.TP
.B \f[B]\-\-jitter\f[] \f[I]arg\f[]
Amount of noise to add to distances
.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.