Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

The history of long‐branch attraction, and in particular methods suggested to detect and
avoid the artifact to date, is reviewed. Methods suggested to avoid LBA‐artifacts include …

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 …

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 …

Abstract Comparison of relative fixation rates of synonymous (silent) and nonsynonymous
(amino acid-altering) mutations provides a means for understanding the mechanisms of …

A new class of distances appropriate for measuring similarity relations between sequences,
say one type of similarity per distance, is studied. We propose a new" normalized …

We present a new method for clustering based on compression. The method does not use
subject-specific features or background knowledge, and works as follows: First, we …

The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

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 …

Abstract We implement a Bayesian Markov chain Monte Carlo algorithm for estimating
species divergence times that uses heterogeneous data from multiple gene loci and …