[HTML][HTML] Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …
How deep is the conflict between molecular and fossil evidence on the age of angiosperms?
The timing of the origin of angiosperms is a hotly debated topic in plant evolution. Molecular
dating analyses that consistently retrieve pre‐Cretaceous ages for crown‐group …
dating analyses that consistently retrieve pre‐Cretaceous ages for crown‐group …
Phylotranscriptomic analysis of the origin and early diversification of land plants
Reconstructing the origin and evolution of land plants and their algal relatives is a
fundamental problem in plant phylogenetics, and is essential for understanding how critical …
fundamental problem in plant phylogenetics, and is essential for understanding how critical …
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 …
Fast coalescent-based computation of local branch support from quartet frequencies
Species tree reconstruction is complicated by effects of incomplete lineage sorting,
commonly modeled by the multi-species coalescent model (MSC). While there has been …
commonly modeled by the multi-species coalescent model (MSC). While there has been …
ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference
Highly divergent sites in multiple sequence alignments (MSAs), which can stem from
erroneous inference of homology and saturation of substitutions, are thought to negatively …
erroneous inference of homology and saturation of substitutions, are thought to negatively …
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
Background The use of transcriptomic and genomic datasets for phylogenetic reconstruction
has become increasingly common as researchers attempt to resolve recalcitrant nodes with …
has become increasingly common as researchers attempt to resolve recalcitrant nodes with …
Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)
Informed management and conservation efforts are vital to sustainable recreational fishing
and biodiversity conservation. Because the taxonomic rank of species is important in …
and biodiversity conservation. Because the taxonomic rank of species is important in …
The gene tree delusion
Higher-level relationships among placental mammals are mostly resolved, but several
polytomies remain contentious. Song et al.(2012) claimed to have resolved three of these …
polytomies remain contentious. Song et al.(2012) claimed to have resolved three of these …