Provided by: bali-phy_3.3+dfsg-1_amd64
trees-distances – Compute autocorrelations or other functions of tree distances.
trees-distances analysis trees-file1 [trees-file2 ...]
Compute autocorrelations or other functions of tree distances.
-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 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
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <email@example.com>.
Benjamin Redelings. Feb 2018 trees-distances(1)