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 …

There is an increasing interest in detecting genes, or genomic regions, that have been
targeted by natural selection. The interest stems from a basic desire to learn more about …

The genomic signatures of positive selection and evolutionary constraints can be detected
by analyses of nucleotide sequences. One of the most widely used programs for this …

The past decade has seen a profound change in the scientific understanding of
reproduction. The traditional view of reproduction as a joint venture undertaken by two …

Detecting positive Darwinian selection at the DNA sequence level has been a subject of
considerable interest. However, positive selection is difficult to detect because it often …

The past decade has seen a major increase in the study of noncoding RNAs (ncRNAs).
However, there remains a great deal of confusion and debate over the levels of functionality …

Since the divergence of humans and chimpanzees about 5 million years ago, these species
have undergone a remarkable evolution with drastic divergence in anatomy and cognitive …

The recent availability of genome-scale genotyping data has led to the identification of
regions of the human genome that seem to have been targeted by selection. These findings …

Although the X chromosome is usually similar to the autosomes in size and cytogenetic
appearance, theoretical models predict that its hemizygosity in males may cause unusual …

The parsimony method of and the maximum likelihood method developed from the work of
are two widely used methods for detecting positive selection in homologous protein coding …