… GTREE software for phylogenomic analysis. Shown above is the GTREE user interface
created by our group to correlate a phylogenetic tree with a multiple sequence alignment and …

… Without an objective understanding of the expected accuracy of individual phylogenetic
tree estimation methods under different conditions, we cannot know whether functional …

… Phylogenomics refers to the inference of historical … to the use of phylogenetic analysis to
infer protein function in multigene … , phylogenomics is becoming synonymous with evolutionary …

… that a phylogenetic approach should be routinely incorporated into orthology inference for
phylogenomics. … that allows automation of orthology inference using a phylogenetic approach. …

… thus can be employed by all phylogenomic inference software. … efficient phylogenomic
inference from supermatrices. PTA consists of the species tree, the set of its induced partition trees…

… masking is not necessary when ML is used to infer the phylogeny, this may reflect the lack of
… of phylogenetic inference method is known to have a major effect on phylogenetic accuracy […

… To integrate the different phylogenetic trees into a phylogenomic supertree, we used either
the majority rule from Consense (Felsenstein, 1989) or CLANN (Creevey and McInerney, …

… a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the
class … Here, we attempt to reconstruct a more reliable phylogenetic tree of Chlorophyta both by …

… The approximately 1.1 million predicted genes yielded a total of 18,607 genes that corresponded
to our 31 protein markers and that were long enough for phylogenetic analysis. Figure …

… partitions assessed by phylogenetic analysis may become … artifacts in a phylogenomic data
set comprising orthologous … or evolutionary rate alone guarantees phylogenetic accuracy, as …