Man page - trees-distances(1)

Packages contains this manual

Package:  bali-phy
apt-get install bali-phy

Manuals in package:
• alignment-consensus(1)
• cut-range(1)
• alignment-thin(1)
• alignment-max(1)
• bali-phy-pkg(1)
• bp-analyze(1)
• alignment-draw(1)
• summarize-ancestors(1)
• extract-ancestors(1)
• stats-select(1)
• mctree-mean-lengths(1)
• trees-consensus(1)
• alignment-find(1)
• bali-phy(1)
• statreport(1)
• alignment-indices(1)
• tree-mean-lengths(1)
• pickout(1)
• draw-tree(1)
• alignment-gild(1)
• alignment-distances(1)
• alignment-info(1)
• tree-tool(1)
• alignments-diff(1)
• trees-bootstrap(1)
• mcon-tool(1)
• alignment-cat(1)
• alignment-chop-internal(1)
• alignment-translate(1)
• trees-distances(1)
• bali-subsample(1)
Documentations in package:
• bali-phy

Manual

trees-distances

NAME
SYNOPSIS
DESCRIPTION
INPUT OPTIONS:
ANALYSIS OPTIONS:
REPORTING BUGS:
AUTHORS

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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, closest, 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.

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