M5.14 - Review of target applications (phylogenetics)

Submitted by Scratchpad Team on Tue, 11/01/2011 - 14:17

A few comments:

  1. Many attempts to contact the Lattice project (http://lattice.umiacs.umd.edu/) have met with no response.
  2. Likewise, attempts to contact LIRMM (http://www.phylogeny.fr/version2_cgi/simple_phylogeny.cgi) has also been unsuccessful.
  3. The Lisbeth software (http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/software/lisbeth) is not yet available for Unix platforms, though as OBOE now includes Windows VMs as available platforms running Lisbeth as a service can be reinvestigated.

We have been investigating a one-click process from data retrieval (molecular) to alignment and phylogenetic analysis along the lines of 2 above. For data retrieval we have experimented with Genbank, for allignment with Clustalw and Mussle, and for phylogenies, Phylip. Automating a seemless process is not straightforward and without risks but we believe it is achievable withing the OBOE framework.