Dickson S. Guedes
I’ve contributed with BioJava by porting the CookBook’s English version to this Wiki, but I’ve introduced to BioJava at 2005, when I’ve started my Bacharel’s thesis using it how a framework to contruct Phylogenetic trees “powered by” Genetic algorithms. So… if all dones right, I’ll presents my tesis at July of 2006… good luck for me.. “:)
Title: Constructing phylogenetics trees from DNA sequences using Genetic Algorithms, using a Web interface
Abstract: A common process in Phylogenetic Systematics is the construction of cladograms - also known as Phylogenetic trees -, which represent the relation of similarity between the studied species, based on different criteria of evaluation. So, nowadays the use of computational tools is very common to consider the DNA sequences as an evaluation criteria, to return a set of consistent information, based on systematic methods that make use of mathematical resources in order to express relations between species in a model. This research demonstrates how was possible to develop a genetic algorithm with a BLOSUM62 substitution matrix to obtain satisfactory results represented in a phylogenetic tree, expressing similarity relations between the input sequences.
Key words: Bioinformatics, Genetics, Phylogeny, Phylogenetic Trees, Genetic Algorithms