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      TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

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      Author(s): 1 , , 2 , 3 , 1
      Publication date (Electronic):
      Journal: BMC Evolutionary Biology
      Publisher: BioMed Central

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          Abstract

          Background

          Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience.

          Results

          TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language.

          Conclusions

          TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

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          Most cited references18

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          Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.

          H Kishino, T Yano, M. Hasegawa (1984)
          A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized least-squares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.3 +/- 11.7, 13.3 +/- 1.5, 10.9 +/- 1.2, 3.7 +/- 0.6, and 2.7 +/- 0.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the pipedal creature Australopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a proto-chimpanzee after the former had developed bipedalism.
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            Comparison of phylogenetic trees

            D.F. Robinson, L.R. Foulds (1981)
            Article 0 comments Cited 644 times – based on 0 reviews     Review now
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              A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy

              M. Sanderson (1997)
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                Author and article information

                Journal
                Journal ID (nlm-ta): BMC Evol Biol
                Title: BMC Evolutionary Biology
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2148
                Publication date Collection: 2004
                Publication date (Electronic): 28 June 2004
                Volume: 4
                Page: 18
                Affiliations
                [1 ]Department of Statistics, University of Munich, Ludwigstr. 33, D-80539 Munich, Germany
                [2 ]Department of Computer Science, University of Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
                [3 ]John von Neumann Institute for Computing, Forschungszentrum Jülich, D-52425 Jülich, Germany
                Article
                Publisher ID: 1471-2148-4-18
                DOI: 10.1186/1471-2148-4-18
                PMC ID: 459214
                PubMed ID: 15222900
                SO-VID: 967ba232-d3c9-493b-b2eb-68a2b08e6186
                Copyright © Copyright © 2004 Jobb et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
                History
                Date received : 16 March 2004
                Date accepted : 28 June 2004
                Categories
                Subject: Software

                ScienceOpen disciplines: Evolutionary Biology
                Data availability:
                ScienceOpen disciplines: Evolutionary Biology

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