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xREI: a phylo-grammar visualization webserver.
Barquist L, Holmes I. Barquist L, et al. Among authors: holmes i. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W65-9. doi: 10.1093/nar/gkn283. Epub 2008 Jun 3. Nucleic Acids Res. 2008. PMID: 18522975 Free PMC article.
Fast statistical alignment.
Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. Bradley RK, et al. Among authors: holmes i. PLoS Comput Biol. 2009 May;5(5):e1000392. doi: 10.1371/journal.pcbi.1000392. Epub 2009 May 29. PLoS Comput Biol. 2009. PMID: 19478997 Free PMC article.
Evolutionary triplet models of structured RNA.
Bradley RK, Holmes I. Bradley RK, et al. Among authors: holmes i. PLoS Comput Biol. 2009 Aug;5(8):e1000483. doi: 10.1371/journal.pcbi.1000483. Epub 2009 Aug 28. PLoS Comput Biol. 2009. PMID: 19714212 Free PMC article.
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