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 and how it modifies biomolecular function and structure, biodiversity and co …
ASTRAL-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 …
can have different trees due to incomplete lineage sorting, modeled by the multi-species …
Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
The development and application of coalescent methods are undergoing rapid changes.
One little explored area that bears on the application of gene-tree-based coalescent …
One little explored area that bears on the application of gene-tree-based coalescent …
[HTML][HTML] ASTRID: accurate species trees from internode distances
P Vachaspati, T Warnow - BMC genomics, 2015 - Springer
Background Incomplete lineage sorting (ILS), modelled by the multi-species coalescent
(MSC), is known to create discordance between gene trees and species trees, and lead to …
(MSC), is known to create discordance between gene trees and species trees, and lead to …
On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods
The estimation of species trees using multiple loci has become increasingly common.
Because different loci can have different phylogenetic histories (reflected in different gene …
Because different loci can have different phylogenetic histories (reflected in different gene …
[HTML][HTML] The performance of coalescent-based species tree estimation methods under models of missing data
Background Estimation of species trees from multiple genes is complicated by processes
such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer …
such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer …
Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
Y Wu - Evolution, 2012 - academic.oup.com
Incomplete lineage sorting can cause incongruence between the phylogenetic history of
genes (the gene tree) and that of the species (the species tree), which can complicate the …
genes (the gene tree) and that of the species (the species tree), which can complicate the …
DISCO: species tree inference using multicopy gene family tree decomposition
Species tree inference from gene family trees is a significant problem in computational
biology. However, gene tree heterogeneity, which can be caused by several factors …
biology. However, gene tree heterogeneity, which can be caused by several factors …
Multispecies coalescent: theory and applications in phylogenetics
Species tree estimation is a basic part of many biological research projects, ranging from
answering basic evolutionary questions (eg, how did a group of species adapt to their …
answering basic evolutionary questions (eg, how did a group of species adapt to their …
[HTML][HTML] A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
L Liu, L Yu, SV Edwards - BMC evolutionary biology, 2010 - Springer
Background Several phylogenetic approaches have been developed to estimate species
trees from collections of gene trees. However, maximum likelihood approaches for …
trees from collections of gene trees. However, maximum likelihood approaches for …