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      The human phylome.

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          Abstract

          Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them.

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          Identification of common molecular subsequences.

          T.F. Smith, M.S. Waterman (1981)
          Article 0 comments Cited 1698 times – based on 0 reviews     Review now
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            Amino acid substitution matrices from protein blocks.

            S Henikoff, J. Henikoff (1992)
            Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
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              BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

              O. Gascuel (1997)
              We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.
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                Author and article information

                Journal
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome biology
                Publisher: Springer Science and Business Media LLC
                ISSN (Electronic): 1474-760X
                ISSN (Print): 1474-7596
                Publication date (Electronic): 2007
                Volume: 8
                Issue: 6
                Affiliations
                [1 ] Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 46013 Valencia, Spain.
                Article
                Publisher Item ID: gb-2007-8-6-r109
                DOI: 10.1186/gb-2007-8-6-r109
                PMC ID: 2394744
                PubMed ID: 17567924
                SO-VID: 08ecd70a-0991-4b99-862e-4550d86b0315
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