[Biojava-l] Need a hand?

[Shailesh L Mistry]

>> 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.