10.5061/DRYAD.K8N14
Larget, Bret
University of Wisconsin-Madison
Data from: The estimation of tree posterior probabilities using
conditional clade probability distributions
Dryad
dataset
2014
posterior probabilities of trees
Bayesian phylogenetics
conditional clade distributions
independence of separated subtrees
2014-01-07T20:49:02Z
en
https://doi.org/10.1093/sysbio/syt014
1216023 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
In this paper I introduce the idea of conditional independence of
separated subtrees as a principle by which to estimate the posterior
probability of trees using conditional clade probability distributions
rather than simple sample relative frequencies. I describe an algorithm
for these calculations and software which implements these ideas. I show
that these alternative calculations are very similar to simple sample
relative frequencies for high probability trees, but are substantially
more accurate for relatively low probability trees. The method allows the
posterior probability of unsampled trees to be calculated when these trees
contain only clades that are in other sampled trees. Furthermore, the
method can be used to estimate the total probability of the set of sampled
trees which provides a measure of the thoroughness of a posterior sample.
cats-dogsAlignment of 1545 bp COX 1 mitochondrial gene for 6 feliforms and
6 caniforms. Original data from NCBI.rodents62 rodents and mammals, 3768
bp. TREEBASE M2481.M336TREE BASE file M336M501TREE BASE file M501M520TREE
BASE file M520M755TREE BASE file M755.M767TREE BASE file M767.M1044TREE
BASE file M1044.M1366TREE BASE file M1366.M1510TREE BASE file
M1510.M1748TREE BASE file M1748.M1809TREE BASE file M1809.M3475TREE BASE
file M3475.appendixAppendices 1-4.