ASTRAL: genome-scale coalescent-based species tree estimation
نویسندگان
چکیده
منابع مشابه
ASTRAL: genome-scale coalescent-based species tree estimation
MOTIVATION Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and speci...
متن کاملSupplementary Material to ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation
3 Experimental Details 16 3.1 Extra trees for Zhong et al. biological dataset . . . . . . . . . 16 3.2 Methods and Commands . . . . . . . . . . . . . . . . . . . . . 16 3.2.1 Gene tree estimation . . . . . . . . . . . . . . . . . . . 16 3.2.2 ASTRAL . . . . . . . . . . . . . . . . . . . . . . . . . 16 3.2.3 BUCKy-pop . . . . . . . . . . . . . . . . . . . . . . . . 17 3.2.4 MRP and MRL . . . . ....
متن کاملASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
MOTIVATION The estimation of species phylogenies requires multiple loci, since different loci can have different trees due to incomplete lineage sorting, modeled by the multi-species coalescent model. We recently developed a coalescent-based method, ASTRAL, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods o...
متن کاملCoalescent-based species tree estimation: a stochastic Farris transform
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene—i.e., the gene trees—may differ from the species phylogeny and 2) the molecular sequences corresponding to each gene often provide limited information about the gene trees themselves. In this paper we consider an approach to species tree recons...
متن کاملSpecies tree estimation using ASTRAL: how many genes are enough?
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted gene tree topologies is ASTRAL. In this paper, we derive theoretical sample complexity results for the number of genes required by ASTRAL to guarantee reconstr...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2014
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btu462