… Our software guenomu estimates the posterior distribution of species trees (rooted, without …
the posterior distributions of gene family topologies, based on all input gene tree distributions. …

… Here we review the formulation of the species tree inference problem in a Bayesian framework
and then describe our new MCMC algorithms. Let |$X_i)$| be the sequence alignment for …

… For example, the species tree of Figure 1A is hard to reconstruct … the Bayesian approach,
we assign a prior on the species trees, f(… The posterior of S and Θ averages over the gene tree …

… Theoretically, we expect the distributions of species network and gene trees to be identical
… When a new species network is proposed, the rebuild-embedding operator proposes a new …

… species tree and data from the genes of interest (eg a distribution of gene trees previously
reconstructed … In the ML or Bayesian framework, we will compute probabilities of scenarios …

… utilize “one-step” Bayesian methods to infer gene trees and the species tree, with the input
data … form of selection with respect to accurately reconstructing gene trees and species trees. …

… , even assuming we can reconstruct the gene phylogenies … hierarchical Bayesian procedure
for species tree estimation, … input a collection of gene trees (posterior distributions or point …

… The present work summarizes the posterior distribution of the species tree splits to infer the
rooted species tree using majority-rule consensus. To implement all calculations, this study …

… species tree—gene tree discordance, compare the most popular methods for species tree
reconstruction, … takes as input posterior gene tree distributions estimated by any Bayesian …

… The impact of data concatenation on the reliability of phylogenetic reconstruction using
plastid data has been neglected likely due to the persistent treatment of ptDNA as a single locus. …