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Simulations of Sequence Evolution: How (Un)realistic They Are and Why.
- Published in:
- Molecular Biology & Evolution, 2024, v. 41, n. 1, p. 1, doi. 10.1093/molbev/msad277
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- Article
Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses.
- Published in:
- eLife, 2023, p. 1, doi. 10.7554/eLife.85993
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- Article
Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale.
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- Molecular Biology & Evolution, 2023, v. 40, n. 2, p. 1, doi. 10.1093/molbev/msac247
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- Article
Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes.
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- Methods in Ecology & Evolution, 2022, v. 13, n. 11, p. 2339, doi. 10.1111/2041-210X.13980
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- Article
Adaptation to host cell environment during experimental evolution of Zika virus.
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- Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03902-y
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- Article
Relative Time Constraints Improve Molecular Dating.
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- Systematic Biology, 2022, v. 71, n. 4, p. 797, doi. 10.1093/sysbio/syab084
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- Article
Nucleotide Usage Biases Distort Inferences of the Species Tree.
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- Genome Biology & Evolution, 2022, v. 14, n. 1, p. 1, doi. 10.1093/gbe/evab290
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- Article
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.
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- Bioinformatics, 2020, v. 36, n. 18, p. 4822, doi. 10.1093/bioinformatics/btaa615
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- Article
CAARS: comparative assembly and annotation of RNA-Seq data.
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- Bioinformatics, 2019, v. 35, n. 13, p. 2199, doi. 10.1093/bioinformatics/bty903
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- Article
RecPhyloXML: a format for reconciled gene trees.
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- Bioinformatics, 2018, v. 34, n. 21, p. 3646, doi. 10.1093/bioinformatics/bty389
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- Article
Accurate Detection of Convergent Amino-Acid Evolution with PCOC.
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- Molecular Biology & Evolution, 2018, v. 35, n. 9, p. 2296, doi. 10.1093/molbev/msy114
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- Article
Efficient Gene Tree Correction Guided by Genome Evolution.
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- PLoS ONE, 2016, v. 11, n. 8, p. 1, doi. 10.1371/journal.pone.0159559
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- Article
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.
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- Systematic Biology, 2016, v. 65, n. 4, p. 726, doi. 10.1093/sysbio/syw021
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- Article
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated.
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- Molecular Biology & Evolution, 2016, v. 33, n. 2, p. 305, doi. 10.1093/molbev/msv249
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- Article
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses.
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- PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0129183
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- Article
Assessing Approaches for Inferring Species Trees from Multi-Copy Genes.
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- Systematic Biology, 2015, v. 64, n. 2, p. 325, doi. 10.1093/sysbio/syu128
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- Article
The Inference of Gene Trees with Species Trees.
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- Systematic Biology, 2015, v. 64, n. 1, p. e42
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- Article
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.
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- Genome Biology, 2014, v. 15, n. 12, p. 120, doi. 10.1186/s13059-014-0549-1
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- Article
Strepsiptera, Phylogenomics and the Long Branch Attraction Problem.
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- PLoS ONE, 2014, v. 9, n. 10, p. 1, doi. 10.1371/journal.pone.0107709
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- Article
Probabilistic Graphical Model Representation in Phylogenetics.
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- Systematic Biology, 2014, v. 63, n. 5, p. 753, doi. 10.1093/sysbio/syu039
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- Article
Efficient Exploration of the Space of Reconciled Gene Trees.
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- Systematic Biology, 2013, v. 62, n. 6, p. 901
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- Article
Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution.
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- Molecular Biology & Evolution, 2013, v. 30, n. 8, p. 1745
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- Article
AN EVALUATION OF THE HYBRID SPECIATION HYPOTHESIS FOR XIPHOPHORUS CLEMENCIAE BASED ON WHOLE GENOME SEQUENCES.
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- Evolution, 2013, v. 67, n. 4, p. 1155, doi. 10.1111/evo.12009
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- Article
A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia.
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- PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0048990
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- Article
Evolution of gene neighborhoods within reconciled phylogenies.
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- Bioinformatics, 2012, v. 28, n. 18, p. i382
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- Article
Efficient Selection of Branch-Specific Models of Sequence Evolution.
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- Molecular Biology & Evolution, 2012, v. 29, n. 7, p. 1861, doi. 10.1093/molbev/mss059
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- Article
Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping.
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- PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0033852
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- Article
NONADAPTIVE EVOLUTION OF MITOCHONDRIAL GENOME SIZE.
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- Evolution, 2011, v. 65, n. 9, p. 2706, doi. 10.1111/j.1558-5646.2011.01322.x
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- Article
Drift and Genome Complexity Revisited.
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- PLoS Genetics, 2011, v. 7, n. 6, p. 1, doi. 10.1371/journal.pgen.1002092
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- Article
Parallel adaptations to high temperatures in the Archaean eon.
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- 2008
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- Letter
Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.
- Published in:
- Nature Reviews Microbiology, 2008, v. 6, n. 3, p. 245, doi. 10.1038/nrmicro1852
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- Article
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs.
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- BMC Evolutionary Biology, 2008, v. 8, p. 1, doi. 10.1186/1471-2148-8-255
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- Article
Phylogenetic Dating and Characterization of Gene Duplications in Vertebrates: The Cartilaginous Fish Reference.
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- Molecular Biology & Evolution, 2004, v. 21, n. 3, p. 580, doi. 10.1093/molbev/msh046
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- Article