>> a) phylogenetic trees - object model for trees, some simple algorithms >> and IO filters
do you mean doing the actual analysis or just reading/writing phylogenetic tree formats and a GUI to view them with? there is already quite a bit of software out there that does this and may be useable (with permission) Tree of Life Project http://tolweb.org/tree/phylogeny.html fastDNAml - Phylogenetic analysis software TreeView - Tree drawing software PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood http://abacus.gene.ucl.ac.uk/software/paml.html PHYLIP is a free package of programs for inferring phylogenies http://evolution.genetics.washington.edu/phylip.html Phylodendron is an application for drawing phylogenetic trees, used in evolutionary biology http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/ Mesquite - A modular system for evolutionary analysis http://spiders.arizona.edu/mesquite/mesquite.html >> b) emboss integration - launch emboss apps either via command line or as >> native methods do you mean biojava ->emboss or biojava->jemboss->emboss? doing this work may also cut out some of the above since PHYLIP can be accessed via emboss/embassy >> We also never got an expression data API up. not sure exactly what it is you need doing here. Please can you elaborate on this. Shelly. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
