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ADAPTSITE: detecting natural selection at single amino acid sites.
Suzuki Y, Gojobori T, Nei M. Suzuki Y, et al. Bioinformatics. 2001 Jul;17(7):660-1. doi: 10.1093/bioinformatics/17.7.660. Bioinformatics. 2001. PMID: 11448887
Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level.
Suzuki Y, Gojobori T, Kumar S. Suzuki Y, et al. Mol Biol Evol. 2009 Oct;26(10):2275-84. doi: 10.1093/molbev/msp133. Epub 2009 Jul 6. Mol Biol Evol. 2009. PMID: 19581348 Free PMC article.
The evolutionary position of nematodes.
Blair JE, Ikeo K, Gojobori T, Hedges SB. Blair JE, et al. BMC Evol Biol. 2002 Apr 8;2:7. doi: 10.1186/1471-2148-2-7. BMC Evol Biol. 2002. PMID: 11985779 Free PMC article.
CIBEX: center for information biology gene expression database.
Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. Ikeo K, et al. C R Biol. 2003 Oct-Nov;326(10-11):1079-82. doi: 10.1016/j.crvi.2003.09.034. C R Biol. 2003. PMID: 14744116
Optimized ancestral state reconstruction using Sankoff parsimony.
Clemente JC, Ikeo K, Valiente G, Gojobori T. Clemente JC, et al. BMC Bioinformatics. 2009 Feb 7;10:51. doi: 10.1186/1471-2105-10-51. BMC Bioinformatics. 2009. PMID: 19200389 Free PMC article.
A method for detecting positive selection at single amino acid sites.
Suzuki Y, Gojobori T. Suzuki Y, et al. Mol Biol Evol. 1999 Oct;16(10):1315-28. doi: 10.1093/oxfordjournals.molbev.a026042. Mol Biol Evol. 1999. PMID: 10563013
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