Category Archives: Research

Science paper on HIV-1 hidden history

We have participated in a Science paper published today on the early spread of HIV-1 from Kinshasa (DRC) around 1920, and the emphasize the role of transportation, social changes and public health campaigns. The early spread and epidemic ignition of … Continue reading

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New collaborative paper on fish C3 evolution

PLoS ONE just published a paper on the C3 complement gene family, in which we collaborated with other groups to characterize its evolution. Interestingly from this side, we found an old C3 duplication common to all teleost fishes. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099673  

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SGWE simulator published in MBE

Our new simulator has been published in MBE: Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories SGWE simulates genome-wide sequence evolution under several substitution models that may change along the genome and the phylogeny, following … Continue reading

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Sampling trip to Cabe Verde (Sal island)

hey, we just came back from another fantastic trip to Cape Verde. This time we went to the Sal Island, where we sampled several populations of Conus snails. We also did some great diving and found very nice nudibranchs.     

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paper on ABC estimation

A new paper on ABC joint estimation of recombination, substitution and dN/dS rates has just been published in Heredity. http://www.nature.com/hdy/journal/v112/n3/abs/hdy2013101a.html

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jmodeltest HPC

Our HPC benchmarking on jModelTest2 has just been published in: The International Journal of High Performance Computing Applications 2014, Vol. 28(1) 112–125 DOI: 10.1177/1094342013495095 The performance evaluation of jModelTest2 on a 40-core shared memory system and on a 528-core cluster has shown … Continue reading

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G3 paper on overlapping genes

Hi, we have published a new paper in the journal G3 on the “Origin and Length Distribution of Unidirectional Prokaryotic Overlapping Genes”. This is freely accessible at http://www.g3journal.org/content/4/1/19.long    

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New paper on structurally constrainted substitution models

Hi, Together with Ugo Bastolla group at UCM, we have published in Bioinformatics a method and accompanying software (https://code.google.com/p/proteinevolver/) to simulate protein evolution taking into consideration structural constraints.   Protein Evolution along Phylogenetic Histories under Structurally Constrained Substitution Models

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New paper on HPC jmodeltest

Hi, A new paper benchmarking  the High Performance Computing version of jmodeltest2 is available online. This is a collaboration with Ramon Doallo’s HPC group at the University of Coruña, and lead by our joint graduate student Diego Darriba. Here we … Continue reading

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