Title	Publication Date	Language	Citations
BEAST: Bayesian evolutionary analysis by sampling trees	2007/01/01	English	9,687
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes	2013/01/01	English	1,062
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments	2010/01/01	English	880
Bayesian inference of population size history from multiple loci	2008/01/01	English	552
Selecting optimal partitioning schemes for phylogenomic datasets	2014/01/01	English	500
Cryptic animal species are homogeneously distributed among taxa and biogeographical regions	2007/01/01		434
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model	2010/01/01	English	409
Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model	2012/01/01	English	392
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes	2014/01/01	English	363
A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree	2013/01/01	English	348
A glimpse on the pattern of rodent diversification: a phylogenetic approach	2012/01/01	English	324
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study	2007/01/01		281
A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits	2011/01/01	English	238
Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution	2007/01/01		233
HaMStR: Profile hidden markov model based search for orthologs in ESTs	2009/01/01	English	215
Exploring power and parameter estimation of the BiSSE method for analyzing species diversification	2013/01/01	English	202
The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands	2008/01/01	English	201
Natural hybridization in heliconiine butterflies: the species boundary as a continuum	2007/01/01		198
A worldwide correlation of lactase persistence phenotype and genotypes	2010/01/01	English	193
Origin and evolution of the RIG-I like RNA helicase gene family	2009/01/01	English	192
The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals	2009/01/01	English	182
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches	2009/01/01	English	181
Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)	2009/01/01	English	175
A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics	2013/01/01	English	173
A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish	2008/01/01	English	172
Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants	2007/01/01	English	170
Phylogenetic relationships and biogeographical patterns in Circum-Mediterranean subfamily Leuciscinae (Teleostei, Cyprinidae) inferred from both mitochondrial and nuclear data	2010/01/01	English	164
Evolution of pigment synthesis pathways by gene and genome duplication in fish	2007/01/01		164
On the origins of arrestin and rhodopsin	2008/01/01	English	162
Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes	2008/01/01	English	160