[HTML][HTML] Eleven grand challenges in single-cell data science
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
Phylogenetic tree building in the genomic age
Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …
IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
Abstract IQ-TREE (http://www. iqtree. org, last accessed February 6, 2020) is a user-friendly
and widely used software package for phylogenetic inference using maximum likelihood …
and widely used software package for phylogenetic inference using maximum likelihood …
ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models
ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular
tools for selecting the best-fit nucleotide and amino acid substitution models, respectively …
tools for selecting the best-fit nucleotide and amino acid substitution models, respectively …
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 …
PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and
models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and …
models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and …
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
J Trifinopoulos, LT Nguyen… - Nucleic acids …, 2016 - academic.oup.com
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for
IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE …
IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE …
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
A Stamatakis - Bioinformatics, 2014 - academic.oup.com
Motivation: Phylogenies are increasingly used in all fields of medical and biological
research. Moreover, because of the next-generation sequencing revolution, datasets used …
research. Moreover, because of the next-generation sequencing revolution, datasets used …
Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation
Proteins have distinct structural and functional constraints at different sites that lead to site-
specific preferences for particular amino acid residues as the sequences evolve …
specific preferences for particular amino acid residues as the sequences evolve …
[HTML][HTML] Improved modeling of compositional heterogeneity supports sponges as sister to all other animals
The relationships at the root of the animal tree have proven difficult to resolve, with the
current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum …
current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum …