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Titolo:
Phylogenetic inferences from molecular sequences: Review and critique
Autore:
Brocchieri, L;
Indirizzi:
Stanford Univ, Dept Math, Stanford, CA 94305 USA Stanford Univ Stanford CA USA 94305 iv, Dept Math, Stanford, CA 94305 USA
Titolo Testata:
THEORETICAL POPULATION BIOLOGY
fascicolo: 1, volume: 59, anno: 2001,
pagine: 27 - 40
SICI:
0040-5809(200102)59:1<27:PIFMSR>2.0.ZU;2-2
Fonte:
ISI
Lingua:
ENG
Soggetto:
AMINO-ACID SUBSTITUTIONS; HORIZONTAL GENE-TRANSFER; DEPENDENT DNA-STRUCTURE; PROTEIN SEQUENCES; MITOCHONDRIAL EVOLUTION; CONFORMATIONAL MAPS; MULTIPLE ALIGNMENT; CONSISTENCY INDEX; BACTERIAL GENOMES; HOMOPLASY EXCESS;
Tipo documento:
Review
Natura:
Periodico
Settore Disciplinare:
Agriculture,Biology & Environmental Sciences
Life Sciences
Citazioni:
102
Recensione:
Indirizzi per estratti:
Indirizzo: Brocchieri, L Stanford Univ, Dept Math, Stanford, CA 94305 USA Stanford Univ Stanford CA USA 94305 Stanford, CA 94305 USA
Citazione:
L. Brocchieri, "Phylogenetic inferences from molecular sequences: Review and critique", THEOR POP B, 59(1), 2001, pp. 27-40

Abstract

Conflicting results often accompany phylogenetic analyses of RNA, DNA, or protein sequences across diverse species. Causes contributing to these conflicts relate to ambiguities in identifying homologous characters of alignments, sensitivity of tree-making methods to unequal evolutionary rates, biases in species sampling, unrecognized paralogy, functional differentiation, loss of phylogenetic informational content due to long branches or fast evolution, and difficulties with the assumptions and approximations used to infer phylogenetic relationships. Attempts to surmount these conflicts by averaging over many proteins are problematic due to inherent biases of selected families, lack of signal in others, and events of lateral transfer, fusion, and/or chimerism. The process of assessing reliability of the results using the bootstrap method is strewn with obstacles because of lack of independence and inhomogeneity in the molecular data. Problems inherent to the three major procedures for developing phylogenetic trees-parsimony, likelihood, distance-are reviewed. Special attention is given to the problem of inferring evolutionary distances from patterns of similarity among sequences. The difficulties encountered by methods of phylogenetic reconstructions based on the analysis of divergent sequence families make new methods based on the analysis of complete genomes reasonable alternatives. Several of these are considered, including the signature sequences of Gupta and associates, the study of genome profiles, and the genomic signature set forth by Karlinand colleagues. (C) 2001 Academic Press..

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Documento generato il 29/03/20 alle ore 00:32:31