Category Archives: Publications

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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New editorial in JME

Hi, a new editorial just came out in the Journal of Molecular Evolution in which I discuss the impact of NGS data in the development of practical models of molecular evolution for phylogenomic reconstruction:   Phylogenetic Models of Molecular Evolution: … Continue reading

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