ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species and removes low support branches from gene trees, resulting in improved accuracy.
ASTRAL: genome-scale coalescent-based species tree estimation
- S. Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. S. Swenson, T. Warnow
- Environmental Science, BiologyBioinform.
- 22 August 2014
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.
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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.
Whole-genome analyses resolve early branches in the tree of life of modern birds
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.
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
This article proposes a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees and evaluates the precision and recall of the local PP on a wide set of simulated and biological datasets.
A communal catalogue reveals Earth’s multiscale microbial diversity
A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
Phylotranscriptomic analysis of the origin and early diversification of land plants
- N. Wickett, S. Mirarab, J. Leebens-Mack
- BiologyProceedings of the National Academy of Sciences
- 29 October 2014
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.
ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches
- Chao Zhang, Erfan Sayyari, S. Mirarab
- Computer ScienceRECOMB Comparative Genomics Satellite Conference
- 4 October 2017
This paper introduces ASTRAL-III, which substantially improves on ASTRal-II in terms of running time by handling polytomies more efficiently, exploiting similarities between gene trees, and trimming unnecessary parts of the search space.
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
- S. Mirarab, Nam-phuong Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, T. Warnow
- Computer Science, BiologyJ. Comput. Biol.
- 30 April 2015
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).
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled.