Provided by: bali-phy_3.3+dfsg-1_amd64

**NAME**

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

**SYNOPSIS**

trees-distancesanalysistrees-file1 [trees-file2 ...]

**DESCRIPTION**

Compute autocorrelations or other functions of tree distances.

**INPUT** **OPTIONS:**

-h,–helpproduce help message-sarg(=0),–skiparg(=0)number of tree samples to skip-uarg,–untilargRead until this number of trees.-marg,–maxargThin tree samples down to this number of trees.-xarg(=1),–subsamplearg(=1)factor by which to subsample-v,–verboseOutput more log messages on stderr.

**ANALYSIS** **OPTIONS:**

–analysisarg(=matrix)Analysis: matrix, autocorrelation, diameter, compare, convergence, converged.–metricarg(=topology)Tree distance: topology, branch, internal-branch.–remove-duplicates[matrix]: disallow zero distances between points.–max-lagarg[autocorrelation]: max lag to consider.–CIarg(=0.95)Confidence interval size.–convergedarg(=0.05)Comma-separated quantiles of distance required for converged? (smaller is more strict).–meanShow mean and standard deviation–medianShow median and confidence interval–minmaxShow minimum and maximum distances–leaves-onlyShow minimum and maximum distances–topology-onlyShow minimum and maximum distances–jitterargAmount 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)