MSA skype 20100608

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Mark, Andreas

Report from last week:

-Mark discussed the design with the 3 Mentors and incorporated feedback into the design.

-The code got committed into the new biojava3-alignment module which will contain all code for the project.


Status of the BioJava Phylo modules?

We currently have two modules for that. One is a legacy module from biojava1, one is the emerging new biojava3 module. Andreas will contact the other Mentors to discuss organization of the code. The forester library source code should be taken out of the new biojava3-phylo module. Andreas will set this up as a .jar file dependency

What is the best code base to convert a similarity matrix to the guide tree?

We will discuss source code options with other Mentors.

Outlook for this week:

- finalize pairwise alignments
- get similarity matrix from pairwise alignments
- depending on the question re phylo modules:  convert similarity matrix to a guide tree…