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Calculating orthologs in bacteria and Archaea: a divide and conquer approach.

Halachev MR, Loman NJ, Pallen MJ.

PLoS One. 2011;6(12):e28388. doi: 10.1371/journal.pone.0028388. Epub 2011 Dec 12.


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.


Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

Wolf YI, Makarova KS, Yutin N, Koonin EV.

Biol Direct. 2012 Dec 14;7:46. doi: 10.1186/1745-6150-7-46.


Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.


A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA.

Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.


A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.

Cortez D, Forterre P, Gribaldo S.

Genome Biol. 2009;10(6):R65. doi: 10.1186/gb-2009-10-6-r65. Epub 2009 Jun 16.


Comparison of RefSeq protein-coding regions in human and vertebrate genomes.

Fong JH, Murphy TD, Pruitt KD.

BMC Genomics. 2013 Sep 25;14:654. doi: 10.1186/1471-2164-14-654.


CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

Zuo G, Hao B.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):321-31. doi: 10.1016/j.gpb.2015.08.004. Epub 2015 Nov 10.


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.


The origins of modern proteomes.

Kurland CG, Canbäck B, Berg OG.

Biochimie. 2007 Dec;89(12):1454-63. Epub 2007 Sep 15.


Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles.

Psomopoulos FE, Mitkas PA, Ouzounis CA.

PLoS One. 2013;8(1):e52854. doi: 10.1371/journal.pone.0052854. Epub 2013 Jan 14.


Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.

Bocs S, Danchin A, Médigue C.

BMC Bioinformatics. 2002;3:5. Epub 2002 Feb 5.


Novel coding regions in four complete archaeal genomes.

Raghavan S, Ouzounis CA.

Nucleic Acids Res. 1999 Nov 15;27(22):4405-8.


The amazing world of bacterial structured RNAs.

Westhof E.

Genome Biol. 2010;11(3):108. doi: 10.1186/gb-2010-11-3-108. Epub 2010 Mar 15. Review.


Retroids in archaea: phylogeny and lateral origins.

Rest JS, Mindell DP.

Mol Biol Evol. 2003 Jul;20(7):1134-42. Epub 2003 May 30.


Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes.

Horimoto K, Fukuchi S, Mori K.

Bioinformatics. 2001 Sep;17(9):791-802.

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