MSA skype 20100629

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Mark, Kyle, Andreas

Weekly update:

Mark: Finished the Smith Waterman implementation and updated the datastructures to store local alignments. Started with data structures for profile profile alignments.

Next steps: Algorithm for profile profile alignment and traversing the tree

Problem with Eclipse

Sometimes the substitution matrices can’t be found from resource folder. Is it a Maven eclipse issue?

Test Coverage

Tried the CodeCover eclipse plugin but there were some issues with it. Would be nice to be able to see how complete the tests are.


Running now at


Kyle: We have a first fork. Andy Yates patched some issues on a branch. Need to make sure the patches are merged back correctly.

Outlook for next week

Mark: plan for this week to have a rough sequence alignment

Travel Plans

Andreas: I will be traveling next two tuesdays, so no regular skype calls, unless there is an emergency. Communication will be via email.