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Category Archives: Publications
A next-generation version of modeltest
The Stamatakis lab as taken over the Modeltest series! check Modeltest-NG. ModelTest-NG is much faster than jModelTest and ProtTest but equally accurate and introduces new features, such as ascertainment bias correction, mixture, and free-rate models, or the automatic processing of … Continue reading
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NGS coverage and evolutionary inferences from single-cells
New paper just out @GenomeMedicine! We report the impact of sequencing depth (and sampling effort) towards variant detection, genotype accuracy, clonal inference and phylogenetic reconstruction from single-cell cancer data. https://rdcu.be/LJ4E
Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish
Congratulations Iria for publishing a very nice paper describing the assembly of the genome of a beautiful angelfish! https://www.nature.com/articles/s41598-018-19430-x
ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability
A new evolutionary framework for ancestral protein reconstruction accounting for structural constraints, just published in Systematic Biology https://academic.oup.com/sysbio/article-abstract/66/6/1054/2840014/ProtASR-An-Evolutionary-Framework-for-Ancestral?redirectedFrom=fulltext
Forensic genetics and genomics: Much more than just a human affair
A comprehensive review on the diverse disciplines of nonhuman forensic genetics, just published in PLoS Genetics. Indeed, it is a fantastic collaboration with the lab of Antonio Amorim and Angel Carracedo: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006960
Heterogeneous recombination among Hepatitis B virus genotypes
A very interesting paper on heterogeneous recombination in Hepatitis B virus, just published in Infection, Genetics and Evolution http://www.sciencedirect.com/science/article/pii/S1567134817302721
Eco-evo classification of tumors
Nice to contribute to this consensus statement in Nature Reviews Cancer about classifying tumors according to their ecological and evolutionary features: http://go.nature.com/2fopLbX
Multiregional tumor trees are not phylogenies
Our comment about misusing multiregional trees in cancer is out: Alves JA, Prieto T, Posada D. 2017. Multiregional tumor trees are not phylogenies. Trends in Cancer: 0.1016/j.trecan.2017.06.004 https://t.co/HVb8dVpi6O Here we show that multiregional tumor trees built from bulk … Continue reading
species tree review in barcode isse
Diego Mallo’s review on species trees in the open access theme issue “From DNA barcodes to biomes” compiled and edited by Paul DN Hebert, Mehrdad Hajibabaei and Peter M Hollingsworth is out. Access content online at bit.ly/PTB1702. The main TOC … Continue reading
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Our paper on comparison of next-generation sequencing simulators is out
Our review paper about next-generation sequencing simulators is out on Nature Reviews Genetics (advance online publication). Escalona M, Rocha S, Posada D (2016). A comparison of tools for the simulation of genomic next-generation sequencing data. Nature Reviews Genetics doi:10.1038/nrg.2016.57 Online … Continue reading
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