ABCC : Applications Web Page

Applications Web Page Welcome to the ABCC Accessible Application Web Page.

From this page, you can get information about our scientific applications and databases. To get more information about any topic, or to run an application, click on any of the menu items on the left-hand side. Program with a tag "Run" is runnable. This site continues to grow, so come back often to check out the many accessible applications available here at the Advanced Biomedical Computing Center (ABCC).

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Phylogenetic Analysis
PAUP
PAUP is designed for phylogenetic analysis using parsimony and other methods.
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LARD
LARD detects and characterizes recombination between DNA sequences using maximum likelihood. LARD is decscribed in detail in the following paper: Holmes, E.C., Worobey, M., and Rambaut, A., 1999 "Phylogenetic Evidence for Recombination in Dengue Virus" Molecular Biology and Evolution 16:405.
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PHYLIP
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters. The programs are controlled through a menu, which asks the users which options they want to set, and allows them to start the computation. The data are read into the program from a text file, which the user can prepare using any word processor or text editor. Some sequence analysis programs such as alignment programs can write data files in the PHYLIP format. Output is written onto special files with names like "outfile" and "treefile". Trees written onto "treefile" are in the Newick format, an informal standard agreed to in 1986 by authors of a number of major phylogeny packages.
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Topal
TOPAL checks for evidence of past recombination events, by looking for changes in the inferred phylogenetic tree topology between adjacent regions of a multiple sequence alignment. It detects recombinations by sliding a window along a sequence alignment, and measuring the discrepancy between the trees suggested by the first and second halves of the window, using distance matrix methods. Topal method is described in: - McGuire, G., F. Wright, and M. J. Prentice. 1997. A graphical method for detecting recombination in phylogenetic data sets. Molecular Biology and Evolution 14: 1125-1131. The TOPAL 2.0 program, and recent changes to the method, are described in: - McGuire, G. and F. Wright. 2000. TOPAL 2.0 : improved detection of mosaic sequences within multiple alignments. Bioinformatics 16: 130-134.
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Modeltest
MODELTEST is program for the selection the model of nucleotide substitution that best fits the data. Currently, the program chooses among 56 models, and calculates AIC values, AIC differences and Akaike weights and hierarchical likelihood ratio tests. This version includes implements assesment of model uncertainty and tools for model averaging using the AIC. A new addition is the calculation of model averaged estimates and parameter importances. Note that it has been observed that this hLRT implementation can get trapped in local optima. Check your results.
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