DiegoDarriba

If brute force doesn't solve your problems,
then you aren't using enough

me

I am an Assistant Professor at Universidade da Coruña as part of the Computer Architecture Group (GAC). Formerly I worked as a postdoc researcher in the Exelixis lab at H-ITS (Heidelberg) and I also colaborated with the Phylogenomics group (UVIGO).

The main topics of my research are Bioinformatics (molecular evolution, genomics and proteomics) and Parallel Computing for both desktop computers and cluster architectures.

Don't hesitate on asking me if you have any question about my research, or you need some advice about how not to choose the colors for your own website. I'll be glad of helping you!

Things I do:

Things you might be interested in:

phylo tree

Teaching

  • Fundamentos de Computadores (Q1/GCED)
  • Estructura de Computadores (Q3/GEI)
  • Concurrencia y Paralelismo (Q4/GEI)
  • Computación Paralela Avanzada (Q2/MHPC)
  • Computación de Altas Prestaciones en Bionformática (Q2/MUBICS)

Software

ModelTest-NG

ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, & Flouri T. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Molecular Biology and Evolution, 37(1), 291-294, 2020

Phylogenetic Likelihood Library

libPLL: The Phylogenetic Likelihood Library is a highly optimized and parallelized library for rapid prototyping and development of likelihood based phylogenetic inference codes. libPLL is the core of RAxML-NG, ModelTest-NG and EPA-NG, among others.

PLL high level modules

High level modular library for libPLL, for handling and operate with MSAs, trees, models, etc.

Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A. Stamatakis A. The phylogenetic likelihood library. Systematic biology, 64(2):356-362, 2014

jModelTest 2

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch lenght), heuristic filtering and automatic logging of user activity.

Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772, 2012

ProtTest 3

ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance (Posada and Buckley 2004). ProtTest differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include likelihood ratio tests, as not all models included in ProtTest are nested.

Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27:1164-1165, 2011

ForeSeqs

ForeSeqs is a tool for predicting sequences in data sets with whole missing partitions. Missing data usually lead to wrong phylogenetic inferences, since branches leading to unexistent taxa can have arbitrary lengths. Terraces in the phylogenetic tree space is another problem derived from missing taxa. Even though this problem can be avoided by linking branch lengths across partitions, the missing data can affect the inferences.

Darriba D, Weiss M, Stamatakis A: Prediction of missing sequences and branch lengths in phylogenomic data. Bioinformatics 32(9):1331-1337, 2016

TreeChar

TreeChar is a tool for characterizing the phylogenetic tree space. Maximum-Likelihood heuristic makes assumptions on the phylogenetic tree space. However, little is known about the effect of the data characteristics on the likelihood surface, as long as it is usually not feasible to evaluate the whole tree space, which grows exponentially with the number of taxa.

Contact

E-Mail

@ diego.darriba [at] udc [dot] es

Computer Architecture Group
Research Center on Information and Communication Technologies (CITIC)
Department of Computer Engineering
Facultade de Informática
Universidade de A Coruña

fic

Postal Address

Facultade de Informática
Universidad de A Coruña
Campus de Elviña s/n
15071 A Coruña
España