[Biojava-l] BioJava implementation of a phylogenetic tree reconstruction algorithm

[Mara Axiom]

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