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Items: 1 to 20 of 145

1.

AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.

Kumar S, Skjaeveland A, Orr RJ, Enger P, Ruden T, Mevik BH, Burki F, Botnen A, Shalchian-Tabrizi K.

BMC Bioinformatics. 2009 Oct 28;10:357. doi: 10.1186/1471-2105-10-357.

2.

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

Löytynoja A, Goldman N.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.

3.

Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.

Glanville JG, Kirshner D, Krishnamurthy N, Sjölander K.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W27-32. Epub 2007 May 8.

4.

PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences.

Hanekamp K, Bohnebeck U, Beszteri B, Valentin K.

Bioinformatics. 2007 Apr 1;23(7):793-801. Epub 2007 Mar 1.

PMID:
17332025
5.
6.

BOV--a web-based BLAST output visualization tool.

Gollapudi R, Revanna KV, Hemmerich C, Schaack S, Dong Q.

BMC Genomics. 2008 Sep 15;9:414. doi: 10.1186/1471-2164-9-414.

7.

BIR Pipeline for Preparation of Phylogenomic Data.

Kumar S, Krabberød AK, Neumann RS, Michalickova K, Zhao S, Zhang X, Shalchian-Tabrizi K.

Evol Bioinform Online. 2015 Apr 27;11:79-83. doi: 10.4137/EBO.S10189. eCollection 2015. Review.

8.

OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences.

Schreiber F, Wörheide G, Morgenstern B.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W185-8. doi: 10.1093/nar/gkp434. Epub 2009 Jun 2.

9.

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

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T.

Bioinformatics. 2009 Aug 1;25(15):1972-3. doi: 10.1093/bioinformatics/btp348. Epub 2009 Jun 8.

10.

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219. doi: 10.1186/1471-2105-10-219.

11.

SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments.

Ajawatanawong P, Atkinson GC, Watson-Haigh NS, Mackenzie B, Baldauf SL.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W340-7. doi: 10.1093/nar/gks561. Epub 2012 Jun 11.

12.

POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis.

Lin CY, Lin FK, Lin CH, Lai LW, Hsu HJ, Chen SH, Hsiung CA.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W553-6.

13.

PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

Pei J, Grishin NV.

Methods Mol Biol. 2014;1079:263-71. doi: 10.1007/978-1-62703-646-7_17.

14.

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

Huerta-Cepas J, Serra F, Bork P.

Mol Biol Evol. 2016 Jun;33(6):1635-8. doi: 10.1093/molbev/msw046. Epub 2016 Feb 26.

15.

Nexplorer: phylogeny-based exploration of sequence family data.

Gopalan V, Qiu WG, Chen MZ, Stoltzfus A.

Bioinformatics. 2006 Jan 1;22(1):120-1. Epub 2005 Nov 2.

16.

TaxMan: a taxonomic database manager.

Jones M, Blaxter M.

BMC Bioinformatics. 2006 Dec 18;7:536.

17.

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

Keane TM, Naughton TJ, McInerney JO.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W33-7. Epub 2007 Jun 6.

18.

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Hartmann S, Vision TJ.

BMC Evol Biol. 2008 Mar 26;8:95. doi: 10.1186/1471-2148-8-95.

19.

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4.

20.

RDP2: recombination detection and analysis from sequence alignments.

Martin DP, Williamson C, Posada D.

Bioinformatics. 2005 Jan 15;21(2):260-2. Epub 2004 Sep 17.

PMID:
15377507

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