Abstract
BackgroundMost analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience.ResultsTREEFINDER 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.ConclusionsTREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.
Highlights
Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience
Available phylogenetic methods The phylogenetic analysis procedures currently implemented in TREEFINDER focus mainly on probabilistic and statistical approaches
The TREEFINDER project is an ongoing effort in providing an easy-to-use and yet powerful platform-independent analysis environment for molecular phylogenetics
Summary
Available phylogenetic methods The phylogenetic analysis procedures currently implemented in TREEFINDER focus mainly on probabilistic and statistical approaches. Simulation of trees and data is useful to assess the accuracy of phylogenetic methods and to generate empirical distributions for test statistics [13,14]. Rate profiles The computation of rate and mutation profiles [15] along sequence alignments is implemented in TREEFINDER These plots are useful in the inference of functional regions and in investigating the selective forces acting on DNA sequences. We conducted a simulation study to investigate the computation time, the accuracy (=probability to recover the exact true tree topology), and the expected dissimilarity of true and inferred tree [21] for several widely used programs and TREEFINDER. It turns out that the accuracy of TREEFINDER with regard to correctly inferring tree topologies and estimating branch lengths is comparable to that of other likelihood programs such as PAUP* and fastDNAML that are often used as "gold standards". These, and other procedures, are scheduled for inclusions in future releases of TREEFINDER
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