Category Archives: Publications

Unsorted Homology within Locus and Species Trees

It is now the turn for printed versions! You can find our penultimate paper in the current version of Systematic Biology (November 2014) . Here we show how classical homology categories can fail to describe homology relationships when we consider … Continue reading

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A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

Our latest article has just been published in Systematic Biology. It describes a model for estimating the set of  species trees conforming to several tree-to-tree distances at once. We show how we can use reconciliation distances, the recently developed mulRF distance, … Continue reading

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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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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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jmodeltest.org in Bioinformatics

We have developed a Cloud implementation of jModelTest2 than can be freely accessed at jmodeltest.org. The Bioinformatics Application Note describing this tool is already available at: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btu032? ijkey=U1UjB3gbQSJDTEe&keytype=ref

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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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