Man page - trees-distances(1)
Packages contas this manual
- alignment-distances(1)
- alignment-max(1)
- bali-phy(1)
- tree-mean-lengths(1)
- mcon-tool(1)
- extract-ancestors(1)
- cut-range(1)
- alignment-indices(1)
- alignment-thin(1)
- stats-select(1)
- pickout(1)
- trees-consensus(1)
- alignment-gild(1)
- alignment-chop-internal(1)
- summarize-ancestors(1)
- draw-tree(1)
- bali-phy-pkg(1)
- mctree-mean-lengths(1)
- tree-tool(1)
- alignment-find(1)
- trees-bootstrap(1)
- alignment-translate(1)
- trees-distances(1)
- alignment-cat(1)
- statreport(1)
- bp-analyze(1)
- alignment-info(1)
- alignment-draw(1)
- alignments-diff(1)
- alignment-consensus(1)
- bali-subsample(1)
Package: bali-phy
apt-get install bali-phy
apt-get install bali-phy
Manuals in package:
Documentations in package:
Manual
| trees-distances(1) | trees-distances(1) |
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.
| Feb 2018 |