USING SUPERTREE ALGORITHM TO INFER A SPECIES TREE FOR A SET OF GENES

Thang Minh Le

Dr. Mariana Kant

Step 1: Prototype for upload a file, execute some modifications in it, display the results file, and download the result file

(done)

Step 2: Create a Web interface for the supertree program such as:

§ the user has the choice to upload a file with a set of constraints or to upload a file with a tree presented in NEXUS format

§ execute the supertree program,

§ the tree-like family is displayed n the list box,

§ the user may download on his/her computer a file with the tree-like family.

(done)

Step 3: Extend the Web interface for the supertree program such as:

§ the user has the choice to upload a file with a mixed representation of the family of trees: set of constraints and NEXUS format

§ execute the supertree program

§ the tree-like family is displayed in the list box

§ the contradictory constraints are displayed also in the list box. They are identified with numbers. The user may choose to have the supertree without deleting the contradictory constraints or to indicate which constraint may be deleted from the set of constraints. This step may be repeated many times.

§ the user may download on his/her computer the file with the supertree and/or the file with the list of contradictory constraints.

(done)