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>.

AUTHORS

       Benjamin Redelings.

                                                    Feb 2018                                  trees-distances(1)