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Items: 1 to 20 of 107

1.

Roundup: a multi-genome repository of orthologs and evolutionary distances.

Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP.

Bioinformatics. 2006 Aug 15;22(16):2044-6.

2.

Roundup 2.0: enabling comparative genomics for over 1800 genomes.

DeLuca TF, Cui J, Jung JY, St Gabriel KC, Wall DP.

Bioinformatics. 2012 Mar 1;28(5):715-6. doi: 10.1093/bioinformatics/bts006.

3.

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

Lin GN, Cai Z, Lin G, Chakraborty S, Xu D.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S5. doi: 10.1186/1471-2105-10-S1-S5.

4.

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Remm M, Storm CE, Sonnhammer EL.

J Mol Biol. 2001 Dec 14;314(5):1041-52.

PMID:
11743721
5.

MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes.

Shi G, Peng MC, Jiang T.

PLoS One. 2011;6(6):e20892. doi: 10.1371/journal.pone.0020892.

6.

BLASTO: a tool for searching orthologous groups.

Zhou Y, Landweber LF.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W678-82.

7.
8.

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

Uchiyama I, Higuchi T, Kawai M.

Nucleic Acids Res. 2010 Jan;38(Database issue):D361-5. doi: 10.1093/nar/gkp948.

9.

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.

10.

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D204-10. doi: 10.1093/nar/gkp1019.

11.

FUNYBASE: a FUNgal phYlogenomic dataBASE.

Marthey S, Aguileta G, Rodolphe F, Gendrault A, Giraud T, Fournier E, Lopez-Villavicencio M, Gautier A, Lebrun MH, Chiapello H.

BMC Bioinformatics. 2008 Oct 27;9:456. doi: 10.1186/1471-2105-9-456.

12.

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.

Auch AF, Henz SR, Holland BR, Göker M.

BMC Bioinformatics. 2006 Jul 19;7:350.

13.

SHOT: a web server for the construction of genome phylogenies.

Korbel JO, Snel B, Huynen MA, Bork P.

Trends Genet. 2002 Mar;18(3):158-62.

PMID:
11858840
14.

Detecting biological network organization and functional gene orthologs.

Cui J, DeLuca TF, Jung JY, Wall DP.

Bioinformatics. 2011 Oct 15;27(20):2919-20. doi: 10.1093/bioinformatics/btr485.

15.

Ortholog detection using the reciprocal smallest distance algorithm.

Wall DP, Deluca T.

Methods Mol Biol. 2007;396:95-110.

PMID:
18025688
16.
17.

webMGR: an online tool for the multiple genome rearrangement problem.

Lin CH, Zhao H, Lowcay SH, Shahab A, Bourque G.

Bioinformatics. 2010 Feb 1;26(3):408-10. doi: 10.1093/bioinformatics/btp689.

18.

Immunity genes and their orthologs: a multi-species database.

Rannikko K, Ortutay C, Vihinen M.

Int Immunol. 2007 Dec;19(12):1361-70.

19.

GeneContent: software for whole-genome phylogenetic analysis.

Gu X, Huang W, Xu D, Zhang H.

Bioinformatics. 2005 Apr 15;21(8):1713-4.

20.

DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection.

Chen TW, Wu TH, Ng WV, Lin WC.

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S6. doi: 10.1186/1471-2105-11-S7-S6.

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