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⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.