TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics - PubMed (original) (raw)

TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

Gangolf Jobb et al. BMC Evol Biol. 2004.

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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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Figures

Figure 1

Figure 1

A typical screenshot of an analysis with TREEFINDER: a tree viewing window showing an inferred maximum-likelihood tree.

Figure 2

Figure 2

TREEFINDER' built-in text editor allows to view and manipulated sequence data sets.

Figure 3

Figure 3

The graphical user interface for tree reconstruction showing the corresponding methods and options available in TREEFINDER.

Figure 4

Figure 4

TREEFINDER's command line terminal, ready for entering TL commands.

Figure 5

Figure 5

An example for an inferred chronogram computed by TREEFINDER using non-parametric rate smoothing [10].

Figure 6

Figure 6

An example for a rate profile, i.e. relative evolutionary rates along an alignment as computed by TREEFINDER.

Figure 7

Figure 7

Comparison of computation times, accuracy and performance of three widely-used likelihood tree reconstruction programs with TREEFINDER.

References

    1. Page RDM, Holmes EC. Molecular Evolution: A Phylogenetic Approach. Oxford: Blackwell Science; 1998.
    1. Felsenstein J. Inferring Phylogenies. Sunderland, MA: Sinauer Associates; 2004.
    1. Swofford DL. PAUP* Phylogenetic analysis using parsimony (* and other methods) Version 4. Sunderland MA: Sinauer Associates; 1998.
    1. Moshier SL. Methods and Programs for Mathematical Functions. Upper Saddle River, New Jersey: Prentice-Hall; 1989.
    1. Lanave C, Preparata G, Saccone C, Serio G. A new method for calculating evolutionary substitution rates. J Mol Evol. 1984;20:86–93. -PubMed

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