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, closest, 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.

AUTHORS

       Benjamin Redelings.

                                                    Feb 2018                                  trees-distances(1)