ABCC 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 mouseover popup 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
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.
Website: Click Here
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.
Website: Click Here
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.
Website: Click Here
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