Cited by ..

The human phylome

Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón

Genome Biol. 2007; 8(6): R109. Published online 2007 June 13. doi: 10.1186/gb-2007-8-6-r109

PMCID:: PMC2394744

Abstract Full Text PDF–491K Supplementary Material

Is Cited by the Following 27 Articles in this Archive:

Phylogenomics-Based Reconstruction of Protozoan Species Tree

Kary A.C.S. Ocaña, Alberto M.R. Dávila

Evol Bioinform Online. 2011; 7: 107–121. Published online 2011 July 31. doi: 10.4137/EBO.S6861

PMCID:: PMC3153122

Abstract Full Text PDF–1.0M Supplementary Material

Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont

Shuji Shigenobu, Alex C. C. Wilson

Cell Mol Life Sci. 2011 April; 68(8): 1297–1309. Published online 2011 March 10. doi: 10.1007/s00018-011-0645-2

PMCID:: PMC3064905

Abstract Full Text PDF–590K Supplementary Material

B2G-FAR, a species-centered GO annotation repository

Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa

Bioinformatics. 2011 April 1; 27(7): 919–924. Published online 2011 February 18. doi: 10.1093/bioinformatics/btr059

PMCID:: PMC3065692

Abstract Full Text PDF–369K Supplementary Material

OrthoInspector: comprehensive orthology analysis and visual exploration

Benjamin Linard, Julie D Thompson, Olivier Poch, Odile Lecompte

BMC Bioinformatics. 2011; 12: 11. Published online 2011 January 10. doi: 10.1186/1471-2105-12-11

PMCID:: PMC3024942

Abstract Full Text PDF–1.4M Supplementary Material

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

Leszek P. Pryszcz, Jaime Huerta-Cepas, Toni Gabaldón

Nucleic Acids Res. 2011 March; 39(5): e32. Published online 2010 December 11. doi: 10.1093/nar/gkq953

PMCID:: PMC3061081

Abstract Full Text PDF–6.4M Supplementary Material

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

Jaime Huerta-Cepas, Salvador Capella-Gutierrez, Leszek P. Pryszcz, Ivan Denisov, Diego Kormes, Marina Marcet-Houben, Toni Gabaldón

Nucleic Acids Res. 2011 January; 39(Database issue): D556–D560. Published online 2010 November 11. doi: 10.1093/nar/gkq1109

PMCID:: PMC3013701

Abstract Full Text PDF–4.3M

Molecular characterization of the evolution of phagosomes

Jonathan Boulais, Matthias Trost, Christian R Landry, Régis Dieckmann, Emmanuel D Levy, Thierry Soldati, Stephen W Michnick, Pierre Thibault, Michel Desjardins

Mol Syst Biol. 2010; 6: 423. Published online 2010 October 19. doi: 10.1038/msb.2010.80

PMCID:: PMC2990642

Abstract Full Text PDF–4.1M Supplementary Material

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

Matthew D. Rasmussen, Manolis Kellis

Mol Biol Evol. 2011 January; 28(1): 273–290. Published online 2010 July 25. doi: 10.1093/molbev/msq189

PMCID:: PMC3002250

Abstract Full Text PDF–756K Supplementary Material

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

The International Aphid Genomics Consortium

PLoS Biol. 2010 February; 8(2): e1000313. Published online 2010 February 23. doi: 10.1371/journal.pbio.1000313

PMCID:: PMC2826372

Abstract Full Text PDF–1.3M Supplementary Material

2× genomes - depth does matter

Michel C Milinkovitch, Raphaël Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldón

Genome Biol. 2010; 11(2): R16. Published online 2010 February 9. doi: 10.1186/gb-2010-11-2-r16

PMCID:: PMC2872876

Abstract Full Text PDF–1.0M

ETE: a python Environment for Tree Exploration

Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón

BMC Bioinformatics. 2010; 11: 24. Published online 2010 January 13. doi: 10.1186/1471-2105-11-24

PMCID:: PMC2820433

Abstract Full Text PDF–623K

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

Marina Marcet-Houben, Giuseppe Marceddu, Toni Gabaldón

BMC Evol Biol. 2009; 9: 295. Published online 2009 December 21. doi: 10.1186/1471-2148-9-295

PMCID:: PMC2803194

Abstract Full Text PDF–1.0M Supplementary Material

Historical Constraints on Vertebrate Genome Evolution

Michel C. Milinkovitch, Raphaël Helaers, Athanasia C. Tzika

Genome Biol Evol. 2010; 2: 13–18. Published online 2009 December 18. doi: 10.1093/gbe/evp052

PMCID:: PMC2839353

Abstract Full Text PDF–357K

Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions

Gregory E. Sims, Se-Ran Jun, Guohong Albert Wu, Sung-Hou Kim

Proc Natl Acad Sci U S A. 2009 October 6; 106(40): 17077–17082. doi: 10.1073/pnas.0909377106

PMCID:: PMC2761373

Abstract Full Text PDF–880K Supplementary Material

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón

Bioinformatics. 2009 August 1; 25(15): 1972–1973. Published online 2009 June 8. doi: 10.1093/bioinformatics/btp348

PMCID:: PMC2712344

Abstract Full Text PDF–57K

Breakpoint graphs and ancestral genome reconstructions

Max A. Alekseyev, Pavel A. Pevzner

Genome Res. 2009 May; 19(5): 943–957. doi: 10.1101/gr.082784.108

PMCID:: PMC2675983

Abstract Full Text PDF–1.8M

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

Marina Marcet-Houben, Toni Gabaldón

PLoS ONE. 2009; 4(2): e4357. Published online 2009 February 3. doi: 10.1371/journal.pone.0004357

PMCID:: PMC2629814

Abstract Full Text PDF–280K Supplementary Material

ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets

Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu

BMC Bioinformatics. 2009; 10(Suppl 1): S5. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S5

PMCID:: PMC2648732

Abstract Full Text PDF–1.2M

metaTIGER: a metabolic evolution resource

John W. Whitaker, Ivica Letunic, Glenn A. McConkey, David R. Westhead

Nucleic Acids Res. 2009 January; 37(Database issue): D531–D538. Published online 2009 January. doi: 10.1093/nar/gkn826

PMCID:: PMC2686446

Abstract Full Text PDF–3.0M

Large-scale assignment of orthology: back to phylogenetics?

Toni Gabaldón

Genome Biol. 2008; 9(10): 235. Published online 2008 October 30. doi: 10.1186/gb-2008-9-10-235

PMCID:: PMC2760865

Abstract Full Text PDF–119K

Protein co-evolution, co-adaptation and interactions

Florencio Pazos, Alfonso Valencia

EMBO J. 2008 October 22; 27(20): 2648–2655. Published online 2008 September 25. doi: 10.1038/emboj.2008.189

PMCID:: PMC2556093

Abstract Full Text PDF–280K

GPCR Genes Are Preferentially Retained after Whole Genome Duplication

Jenia Semyonov, Jae-Il Park, Chia Lin Chang, Sheau Yu Teddy Hsu

PLoS ONE. 2008; 3(4): e1903. Published online 2008 April 2. doi: 10.1371/journal.pone.0001903

PMCID:: PMC2270905

Abstract Full Text PDF–341K Supplementary Material

TreeFam: 2008 Update

Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin

Nucleic Acids Res. 2008 January; 36(Database issue): D735–D740. Published online 2008 January. doi: 10.1093/nar/gkm1005