Fastphylo: Fast tools for phylogenetics

DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics, and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-med...

State aggregation for fast likelihood computations in phylogenetics

Codon models are widely used to identify the signature of selection at the molecular level and to test for changes in selective pressure during the evolution of genes encoding proteins. The large dimensionality of the Markov processes used to model codon evolution makes it difficult to use these models with large biological datasets. We propose here to use state aggregation to reduce the dimens...

Tools for Fast Sequence Alignments

ShatterPlots: Fast Tools for Mining Large Graphs

Graphs appear in several settings, like social networks, recommendation systems, computer communication networks, gene/protein biological networks, among others. A deep, recurring question is “What do real graphs look like?” That is, how can we separate real ones from synthetic or real graphs with masked portions? The main contribution of this paper is ShatterPlots, a simple and powerful algori...

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular stand-alone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists ...