Unfortunately it is impossible to ever conclusively

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Unformatted text preview: be quan?fied. •  Given a set of gene sequences, it should be possible to reconstruct the evolu?onary rela?onships among genes and among organisms. Disclaimers •  This area of computa?onal biology is an intellectual minefield! •  Neither the theory nor the prac?cal applica?ons of any algorithms are universally accepted throughout the scien?fic community •  The applica?on of different sokware packages to a data set is very likely to give different answers Types of Trees A natural model to consider is that of rooted trees Orthologs vs. Paralogs •  When comparing gene sequences, it is important to dis?nguish between iden?cal vs. merely similar genes in different organisms. •  Orthologs are homologous genes in different species with analogous func?ons. •  Paralogs are similar genes that are the result of a gene duplica?on. –  A phylogeny that includes both orthologs and paralogs is likely to be incorrect. –  Some?mes phylogene?c analysis is the best way to determine if a new gene is an ortholog or paralog to other known genes. Are there “Correct Trees”? •  Despite all of these caveats, it is actually quite simple to use computer programs calculate phylogene?c trees for data sets. •  Provided the data are clean, outgroups are correctly specified, appropriate algorithms are chosen, no assu...
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