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ASTRAL: genome-scale coalescent-based species tree estimation
TLDR
ASTRAL is a fast method for estimating species trees from multiple genes that is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. Expand
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
TLDR
A new version of ASTRAL is presented, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods on the datasets the authors examined, and has substantially better accuracy under some conditions. Expand
Whole-genome analyses resolve early branches in the tree of life of modern birds
TLDR
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea. Expand
SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.
TLDR
A modification to the original SATé algorithm that improves upon SATé (which is now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy, and presents two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. Expand
Chemical Phylogenetics of Histone Deacetylases
TLDR
The synthesis and study of a focused library of cinnamic hydroxamates allowed the identification of a first non-selective HDAC inhibitor, which will guide a more informed use of HDAC inhibitors as chemical probes and therapeutic agents. Expand
Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
TLDR
SATé (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion, is presented, showing that coestimation can be both rapid and accurate in phylogenetic studies. Expand
Phylotranscriptomic analysis of the origin and early diversification of land plants
TLDR
Strong and robust support is found for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated. Expand
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
TLDR
A study on biological and simulated data with up to 200,000 sequences is presented, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). Expand
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.
TLDR
A study to evaluate MP-EST-one of the most popular species tree estimation methods designed to address ILS-as well as concatenation under maximum likelihood, the greedy consensus, and two supertree methods (Matrix Representation with Parsimony and Matrix representation with Likelihood). Expand
Indo‐European and Computational Cladistics
TLDR
An attempt to recover the first-order subgrouping of the Indo-European family using a new computational method devised by the authors and based on a ‘perfect phylogeny’ algorithm is reported. Expand
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