trees-distances

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.