20.500.12556/RUL-29476 Implementacija metode asimetričnega srednjega drevesa za iskanje konsenza filogenetskih dreves diplomsko delo Implementation of asymmetric median tree method for the computation of a consensus phylogenetic tree Filogenetsko drevo prikazuje evolucijska razmerja med taksonomskimi enotami. Danes jih gradimo programsko z uporabo različnih metod in na podlagi različnih virov podatkov (npr., zaporedja DNA ali RNA). To mnogokrat privede do nasprotujočih si evolucijskih hipotez, ki jih nato skušamo združiti v eno samo hipotezo oziroma konsenzno drevo. V diplomskem delu je obravnavana konsenzna metoda asimetričnega srednjega drevesa. Le-ta in še dve aproksimacijski metodi so bile implementirane v odprtokodnem paketu Biopython. Uspešnost metode asimetričnega srednjega drevesa je bila primerjana z uspešnostjo metod za gradnjo striktnega, večinskega in Adamsovega konsenza, na nekaj umetnih in enem dejanskem primeru. Pridobljena drevesa so bila ovrednotena z uporabo Robinson-Fouldsove mere in mere razrešenosti drevesa. Asimetrično srednje drevo je velikokrat najmanj podobno vhodnim drevesom, a hkrati najbolj razrešeno drevo, saj podaja največ informacije o evolucijskih razmerjih med taksonomskimi enotami. A phylogenetic tree displays evolutionary relationships between taxonomical units. Nowadays, they are constructed programmatically by using different methods of inference and relying on various data sources, such as DNA and RNA sequences. The resulting evolutionary hypotheses are often contradictory, and need to be resolved by applying consensus methods. In this thesis, asymmetric median tree method (AMT) for construction of consensus phylogenetic trees is described, and along with two other approximation methods implemented in Biopython. AMT was compared to methods of strict, majority and Adams consensus trees on a number of artificial and one real data set. The comparisons were evaluated using the Robinson-Foulds and the tree resolution metrics. The results show that AMT is often the least similar to the input trees. At the same time, it is the most resolved tree, and therefore it offers the most information about evolutionary history of taxonomical units. konsenz drevo filogenetika asimetrično srednje drevo Biopython Robinson-Fouldsova mera consensus tree phylogeny asymmetric median tree Biopython Robinson–Foulds distance true false false Slovenski jezik Angleški jezik Diplomsko delo/naloga 2014-09-17 14:35:04 2014-09-17 14:35:04 2024-08-13 09:27:30 0000-00-00 00:00:00 2014 0 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 14329 1536122051 63100344-20140909125332-diploma.pdf 63100344-20140909125332-diploma.pdf 1 68CAF1102A7E6A69DF848979B7665274 62b13d7fe67777bf7605bd17369e1cde726cb53e5a67b4bf6c7a1feed16da599 4ae7b1ba-a1a8-11eb-a523-00155dcfd717 20.500.12556/rul/211e2855-36ca-4881-8518-d2ecf77e4074 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=29472 Fakulteta za računalništvo in informatiko 0 0 0