Man page - trees-bootstrap(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-bootstrap

NAME
SYNOPSIS
DESCRIPTION
INPUT OPTIONS:
BLOCK BOOTSTRAP OPTIONS:
REPORTING OPTIONS:
REPORTING BUGS:
AUTHORS

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NAME

trees-bootstrap - Compare support for partitions between different files.

SYNOPSIS

trees-bootstrap file1 [ file2 ... ] –predicates predicate file [OPTIONS]

DESCRIPTION

Compare support for partitions between different files.

INPUT OPTIONS:

-h , –help

Produce help message.

-s arg (=10%), –skip arg (=10%)

Number of trees 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 , –subsample arg

Factor by which to sub-sample.

–predicates arg

Predicates to examine.

–min-support arg (=0.1)

Minimum value of predicates to consider interesting..

-V , –verbose

Output more log messages on stderr.

BLOCK BOOTSTRAP OPTIONS:

–bootstrap

Do block bootstrapping to get a CI on the posterior probabilities.

–samples arg (=10000)

Number of bootstrap samples.

–pseudocount arg (=1)

Extra 0/1 to add to bootstrap samples.

–blocksize arg

Block size to use in block boostrap.

–seed arg

Random seed.

REPORTING OPTIONS:

–separation arg (=0)

Only report trees/partitions if they differ by this many LODs

–confidence arg (=0.95)

Width of confidence intervals

–LOD-table arg

Write the partitions LOD10’s to a file.

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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