NAME

trees-distances -- Compute autocorrelations or other functions of tree distances.

SYNOPSIS

trees-distances analysis trees-file1 [trees-file2 ...]

DESCRIPTION

Compute autocorrelations or other functions of tree distances.

INPUT OPTIONS:

-h, --help
produce help message
-s arg (=0), --skip arg (=0)
number of tree samples to skip
-u arg, --until arg
Read until this number of trees.
-m arg, --max arg
Thin tree samples down to this number of trees.
-x arg (=1), --subsample arg (=1)
factor by which to subsample
-v, --verbose
Output more log messages on stderr.

ANALYSIS OPTIONS:

--analysis arg (=matrix)
Analysis: matrix, autocorrelation, diameter, compare, convergence, converged.
--metric arg (=topology)
Tree distance: topology, branch, internal-branch.
--remove-duplicates
[matrix]: disallow zero distances between points.
--max-lag arg
[autocorrelation]: max lag to consider.
--CI arg (=0.95)
Confidence interval size.
--converged arg (=0.05)
Comma-separated quantiles of distance required for converged? (smaller is more strict).
--mean
Show mean and standard deviation
--median
Show median and confidence interval
--minmax
Show minimum and maximum distances
--leaves-only
Show minimum and maximum distances
--topology-only
Show minimum and maximum distances
--jitter arg
Amount of noise to add to distances

REPORTING BUGS:

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.