Hello all, Does anyone have BioJava implementation of a phylogenetic tree reconstruction algorithm, except neighbor-joining or UPGMA? I need this for a research. We have neighbor-joining or UPGMA implementation already, and we want to look at other algorithms other than these. I am new to BioJava, any information will help.
Here is what we want. 1 - Compare sequences in a FASTA file, and find sequences that are similar to each other. 2 - Construct the tree. 3 - Output the tree in Newick (XML will work too) format. In particular we are interested in implementation of BNNP ( http://www.cs.cmu.edu/~guyb/papers/SDBHRS06.pdf) and Align Free ( http://www.math.ucla.edu/~roch/research_files/align-free.pdf) algorithms, but we are open to other algorithms too. Please do not recommend a P-tree reconstruction tool. We are only interested in a source code to meet our specific purpose. Thanks in advance, Mara _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
