Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total). AVAILABILITY AND IMPLEMENTATION: ftp://ftp.vital-it.ch/tools/FastCodeML/ CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.

Selectome update: quality control and computational improvements to a database of positive selection.

Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have benchmarked and implemented a thorough quality control procedure on multiple sequence alignments, aiming to provide minimum false-positive results. We have also improved the computational efficiency of the branch-site test implementation, allowing larger data sets and more frequent updates. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees. A total of 6810 gene trees have some evidence of positive selection. Finally, the web interface has been improved to be more responsive and to facilitate searches and browsing.

On the elusive nature of the Letters from the Heart effect.

The Letters from the Heart effect described by Van den Bergh, Vrana, and Eelen in 1990 is the finding that, in a forced-choice affective evaluation paradigm, typists prefer nonmeaningful letter combinations typed with different fingers over those typed with the same finger, whereas no such preference is evident for nontypists. Typists' dislike of same-finger letter combinations may arise through subconscious activation of motor-behavior memory in affective evaluation tasks, which in turn may create conflicting qualities for same-finger letter combinations given the motor incompatibilities associated with these. Although the effect is cited in the literature, the original finding has never been replicated. The present research attempted to replicate the effect in a series of five studies, involving new sets of letter combinations and a total of 134 typists and 152 nontypists. The effect was not dearly replicated in these studies and thus seems to be elusive. The consistent nonreplication is discussed in terms of a lack of necessary boundary conditions for the effect to emerge reliably and in differences in analysis between the original investigation and the present re-