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Items: 1 to 20 of 143

1.

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. Epub 2012 Jan 13.

2.

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. Epub 2006 Jun 15.

PMID:
16777906
3.

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.

Biol Direct. 2007 Nov 27;2:33.

4.

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. Epub 2011 Aug 19.

5.
6.

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
7.

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.

8.

QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence.

Yu C, Desai V, Cheng L, Reifman J.

BMC Bioinformatics. 2012 Jun 22;13:143. doi: 10.1186/1471-2105-13-143.

9.

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.

Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, Seppey M, Loetscher A, Kriventseva EV.

Nucleic Acids Res. 2017 Jan 4;45(D1):D744-D749. doi: 10.1093/nar/gkw1119. Epub 2016 Nov 28.

10.

MBGD: microbial genome database for comparative analysis.

Uchiyama I.

Nucleic Acids Res. 2003 Jan 1;31(1):58-62.

11.

Identifying single copy orthologs in Metazoa.

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P.

PLoS Comput Biol. 2011 Dec;7(12):e1002269. doi: 10.1371/journal.pcbi.1002269. Epub 2011 Dec 1.

12.

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Wu M, Scott AJ.

Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.

PMID:
22332237
13.

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.

Podell S, Gaasterland T, Allen EE.

BMC Bioinformatics. 2008 Oct 7;9:419. doi: 10.1186/1471-2105-9-419.

14.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli SV, White O, Botstein D, Dolinski K.

PLoS One. 2007 Aug 22;2(8):e766.

15.

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation.

Grazziotin AL, Koonin EV, Kristensen DM.

Nucleic Acids Res. 2017 Jan 4;45(D1):D491-D498. doi: 10.1093/nar/gkw975. Epub 2016 Oct 26.

16.

Computational methods for Gene Orthology inference.

Kristensen DM, Wolf YI, Mushegian AR, Koonin EV.

Brief Bioinform. 2011 Sep;12(5):379-91. doi: 10.1093/bib/bbr030. Epub 2011 Jun 19.

17.
18.

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.

Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A.

Bioinformatics. 2010 Jun 15;26(12):1481-7. doi: 10.1093/bioinformatics/btq229. Epub 2010 May 2.

19.

Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses.

Boyer M, Madoui MA, Gimenez G, La Scola B, Raoult D.

PLoS One. 2010 Dec 2;5(12):e15530. doi: 10.1371/journal.pone.0015530.

20.

PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K.

Plant Cell. 2009 Dec;21(12):3718-31. doi: 10.1105/tpc.109.071506. Epub 2009 Dec 29.

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