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