Almost all protein database search methods use amino acid substitution matrices for
scoring, optimizing, and assessing the statistical significance of sequence alignments. Much …

Osteoarthritis (OA) has long been viewed as a degenerative disease of cartilage, but
accumulating evidence indicates that inflammation has a critical role in its pathogenesis. In …

Insects are the most speciose group of animals, but the phylogenetic relationships of many
major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein …

Background Although draft genomes are available for most agronomically important plant
species, the majority are incomplete, highly fragmented, and often riddled with assembly …

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance
computing) is a sequential and parallel program for inference of large phylogenies with …

Proportional and separate models able to apply different combination of substitution rate
matrix (SRM) and among‐site rate variation model (ASRVM) to each locus are frequently …

Amino acid replacement matrices are an essential basis of protein phylogenetics. They are
used to compute substitution probabilities along phylogeny branches and thus the likelihood …

Using an appropriate model of amino acid replacement is very important for the study of
protein evolution and phylogenetic inference. We have built a tool for the selection of the …

TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic
analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964–969, 1996) …

Our understanding of the origins, the functions and/or the structures of biological sequences
strongly depends on our ability to decipher the mechanisms of molecular evolution. These …