PhyloExplorer: A web server to validate, explore and query phylogenetic trees

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Ranwez, Vincent ^a   Clairon, Nicolas ^a   Delsuc, Frédéric ^a   Pourali, Saeed ^a,b   Auberval, Nicolas ^a   Diser, Sorel ^a   Berry, Vincent ^b  

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^b LIRMM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; INFORMATION PROCESSING; INTERNET; PHYLOGENETIC TREE; TAXONOMY; VALIDATION STUDY; COMPUTER INTERFACE; GENETIC DATABASE; PHYLOGENY;

DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; INTERNET; PHYLOGENY; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 67049167075     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-108     Document Type: Article

References (38)

1. A Taxonomic Search Engine: federating taxonomic databases using web services. RD Page, BMC Bioinformatics 2005 6 48 15757517 10.1186/1471-2105-6-48
2. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. MJ Sanderson MJ Donoghue W Piel T Eriksson, Amer Jour Bot 1994 81 183 10.2307/2445299
3. TBMap: a taxonomic perspective on the phylogenetic database TreeBASE. RD Page, BMC Bioinformatics 2007 8 158 17511869 10.1186/1471-2105-8-158
4. The challenge of constructing large phylogenetic trees. MJ Sanderson AC Driskell, Trends in Plant Science 2003 8 374 379 10.1016/S1360-1385(03)00165-1 12927970
5. Hovergen a Database of Homologous Vertebrate Genes. L Duret D Mouchiroud M Gouy, Nucleic Acids Research 1994 22 2360 2365 8036164 10.1093/nar/22.12.2360 (Pubitemid 24209546)
6. TreeFam: 2008 update. J Ruan H Li ZZ Chen A Coghlan LJM Coin Y Guo JK Heriche YF Hu K Kristiansen RQ Li, Nucleic Acids Research 2008 36 D735 D740 18056084 10.1093/nar/gkm1005
7. OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. V Ranwez F Delsuc S Ranwez K Belkhir MK Tilak EJ Douzery, BMC Evol Biol 2007 7 241 18053139 10.1186/1471-2148-7-241
8. Ensembl 2009. TJP Hubbard BL Aken S Ayling B Ballester K Beal E Bragin S Brent Y Chen P Clapham L Clarke, Nucleic Acids Research 2009 37 D690 D697 10.1093/nar/gkn828 19033362
9. Database resources of the National Center for Biotechnology Information. DL Wheeler C Chappey AE Lash DD Leipe TL Madden GD Schuler TA Tatusova BA Rapp, Nucleic Acids Res 2000 28 10 14 10592169 10.1093/nar/28.1.10 (Pubitemid 30047702)
10. Catalogue of Life: 2008 Annual Checklist. http://www.catalogueoflife.org
11. ITIS: Integrated Taxonomic Information System. http://www.itis.gov
12. Django: a High-level Python Web framework. http://www.djangoproject.com
13. MySQL: the World's Most Popular Open Source Database. http://www.mysql.com
14. CherryPy: a Pythonic, Object-oriented HTTP Framework. http://www.cherrypy.org
15. NetworkX: a Python Package for the Creation, Manipulation, and Study of the Structure, Dynamics, and Functions of Complex Networks. http://networkx. lanl.gov
16. PHY.FI: fast and easy online creation and manipulation of phylogeny color figures. J Fredslund, BMC Bioinformatics 2006 7 315 16792795 10.1186/1471-2105-7-315
17. PhyloWidget: web-based visualizations for the tree of life. GE Jordan WH Piel, Bioinformatics 2008 24 1641 1642 10.1093/bioinformatics/btn235 18487241
18. Wikispecies: a Free Directory of Life. http://species.wikimedia.org
19. Wikipedia: the Free Encyclopedia. http://www.wikipedia.org/
20. CeCILL: Licence Française de Logiciel Libre. http://www.cecill. info/index.en.html
21. TreeView: an application to display phylogenetic trees on personal computers. RD Page, Comput Appl Biosci 1996 12 357 358 8902363
22. TreeDyn: towards dynamic graphics and annotations for analyses of trees. F Chevenet C Brun AL Banuls B Jacq R Christen, BMC Bioinformatics 2006 7 439 17032440 10.1186/1471-2105-7-439
23. Dendroscope: An interactive viewer for large phylogenetic trees. DH Huson DC Richter C Rausch T Dezulian M Franz R Rupp, BMC Bioinformatics 2007 8 460 18034891 10.1186/1471-2105-8-460
24. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. I Letunic P Bork, Bioinformatics 2007 23 127 128 10.1093/bioinformatics/btl529 17050570
25. PhyloFinder: an intelligent search engine for phylogenetic tree databases. D Chen JG Burleigh MS Bansal D Fernandez-Baca, BMC Evol Biol 2008 8 90 18366717 10.1186/1471-2148-8-90
26. Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. D Dalevi TZ Desantis J Fredslund GL Andersen VM Markowitz P Hugenholtz, BMC Bioinformatics 2007 8 402 17949484 10.1186/1471-2105-8-402
27. Interactive visualization software for exploring phylogenetic trees and clades. M Derthick, Bioinformatics 2008 24 868 869 10.1093/bioinformatics/btn038 18263642
28. Clann: investigating phylogenetic information through supertree analyses. CJ Creevey JO McInerney, Bioinformatics 2005 21 390 392 10.1093/bioinformatics/ bti020 15374874
29. The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. MJ Sanderson D Boss D Chen KA Cranston A Wehe, Syst Biol 2008 57 335 346 10.1080/10635150802158688 18570030
30. iSpecies: a Species Search Engine. http://ispecies.org
31. Broad phylogenomic sampling improves resolution of the animal tree of life. CW Dunn A Hejnol DQ Matus K Pang WE Browne SA Smith E Seaver GW Rouse M Obst GD Edgecombe, Nature 2008 452 745 749 10.1038/nature06614 18322464
32. Tunicates and not cephalochordates are the closest living relatives of vertebrates. F Delsuc H Brinkmann D Chourrout H Philippe, Nature 2006 439 965 968 10.1038/nature04336 16495997
33. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. B Roure N Rodriguez-Ezpeleta H Philippe, BMC Evol Biol 2007 7 Suppl 1 S2 17288575 10.1186/1471-2148-7-S1-S2
34. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. F Delsuc M Scally O Madsen MJ Stanhope WW de Jong FM Catzeflis MS Springer EJP Douzery, Molecular Biology and Evolution 2002 19 1656 1671
35. Estimating diversification rates from phylogenetic information. RE Ricklefs, Trends Ecol Evol 2007 22 601 610 10.1016/j.tree.2007.06.013 17963995
36. The NCBI Trace Archives. http://www.ncbi.nlm.nih.gov/Traces/home/
37. The NCBI Taxonomy Browser. http://www.ncbi.nlm.nih.gov/Taxonomy/
38. Animal Diversity Web. http://animaldiversity.ummz.umich.edu/site/index. html