Widespread introgression across a phylogeny of 155 Drosophila genomes
Genome-scale sequence data have invigorated the study of hybridization and introgression,
particularly in animals. However, outside of a few notable cases, we lack systematic tests for …
particularly in animals. However, outside of a few notable cases, we lack systematic tests for …
Understanding phylogenetic incongruence: lessons from phyllostomid bats
All characters and trait systems in an organism share a common evolutionary history that
can be estimated using phylogenetic methods. However, differential rates of change and the …
can be estimated using phylogenetic methods. However, differential rates of change and the …
Highly contiguous assemblies of 101 drosophilid genomes
Over 100 years of studies in Drosophila melanogaster and related species in the genus
Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high …
Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high …
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
We present TranslatorX, a web server designed to align protein-coding nucleotide
sequences based on their corresponding amino acid translations. Many comparisons …
sequences based on their corresponding amino acid translations. Many comparisons …
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
A Stamatakis - Bioinformatics, 2006 - academic.oup.com
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance
computing) is a sequential and parallel program for inference of large phylogenies with …
computing) is a sequential and parallel program for inference of large phylogenies with …
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding
aligned protein sequences. Such codon alignments can be used to evaluate the type and …
aligned protein sequences. Such codon alignments can be used to evaluate the type and …
Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama
The assembly of DNA barcode libraries is particularly relevant within species-rich natural
communities for which accurate species identifications will enable detailed ecological …
communities for which accurate species identifications will enable detailed ecological …
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons
Until now the most efficient solution to align nucleotide sequences containing open reading
frames was to use indirect procedures that align amino acid translation before reporting the …
frames was to use indirect procedures that align amino acid translation before reporting the …
Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice
Background & Aims Alcoholic liver disease is a leading cause of mortality. Chronic alcohol
consumption is accompanied by intestinal dysbiosis, and development of alcoholic liver …
consumption is accompanied by intestinal dysbiosis, and development of alcoholic liver …
ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments
Constructing multiple homologous alignments for protein-coding DNA sequences is crucial
for a variety of bioinformatic analyses but remains computationally challenging. With the …
for a variety of bioinformatic analyses but remains computationally challenging. With the …