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.