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‎_wikis/BioJava:PhyloSOC07.md‎

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Input: Read Nexus File & Extract MATRIX data (Align sequences & decide
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informative sites)
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Day 5: Code for Maximum Parsimony Method (2) -to be worked out
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Day 5: Code for Maximum Parsimony Method (2) -changing plans
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Building Data Structure : decide all possible tree structures &
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initialize variables for those trees.
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Building Data Structure : decide all possible tree structures &
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initialize variables for those trees.
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Day 2: Code for Maximum Parsimony Method (3) - still working on as 16th
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Jul.
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iterate the calculation to dicide a tree
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Day 2: Code for Maximum Parsimony Method (3) - changing plans iterate
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the calculation to dicide a tree
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Day 3: Revising AddTree & getTreeAsJGraphT method (to allow both
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weighted/unweighted tree) - done
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Day 4: Debugging for non-symmetric tree structure (1) - to be worked out
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Day 5: Debugging for non-symmetric tree structure (2) - to be worked out
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Day 4: Debugging for non-symmetric tree structure (1) - done Day 5:
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Debugging for non-symmetric tree structure (2) - done
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<Algorithm> 1. aligning sequences
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*Week 9 Maximum Parsimony Method*
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Day 1: Debugging for AddTreeMethod (for the non-symmetric tree
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structure)
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structure) -done
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Day 2: Debugging for AddTreeMethod (for the non-symmetric tree
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structure)
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structure) -done
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Day 3: Maximum Parsimony Method - solve the problem w/ \# of trees
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Day 4: Maximum Parsimony Method - getting help for Jgrapht type array
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Day 5: Maximum Parsimony Method - finalize
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Day 5: Maximum Parsimony Method -
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- Plan for Maximum Parsimony Method has been changed!
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------------------------------------------------------------------------
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**Part IV : Maximum Likelihood**
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*Week 10 Maximum Parsimony Method*
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------------------------------------------------------------------------
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Day 1: Debugging AddTree Method & commit the source code
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Day 2: PHYLIP installation & learning how to use it
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Day 3: Practicing PHYLIP with MP/ML/Bootstrap methods
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Day 4: Developing the wrapper for PHYLIP MP method (1) - parser
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Day 5: Developing the wrapper for PHYLIP MP method (2) - builing objects
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from the output
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**Part IV : Maximum Likelihood**
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------------------------------------------------------------------------
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*Week 10 Maxumum Likelihood Method*
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*Week 11 Maxumum Likelihood Method*
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1. aligning sequences
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‎_wikis/BioJava:PhyloSOC07.mediawiki‎

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(Align sequences & decide informative sites)
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Day 5: Code for Maximum Parsimony Method (2) -to be worked out
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Day 5: Code for Maximum Parsimony Method (2) -changing plans
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Building Data Structure :
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decide all possible tree structures & initialize variables for those trees.
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Building Data Structure :
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decide all possible tree structures & initialize variables for those trees.
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Day 2: Code for Maximum Parsimony Method (3) - still working on as 16th Jul.
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Day 2: Code for Maximum Parsimony Method (3) - changing plans
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iterate the calculation to dicide a tree
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Day 3: Revising AddTree & getTreeAsJGraphT method (to allow both weighted/unweighted tree) - done
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Day 4: Debugging for non-symmetric tree structure (1) - to be worked out
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Day 5: Debugging for non-symmetric tree structure (2) - to be worked out
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Day 4: Debugging for non-symmetric tree structure (1) - done
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Day 5: Debugging for non-symmetric tree structure (2) - done
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''Week 9 Maximum Parsimony Method''
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Day 1: Debugging for AddTreeMethod (for the non-symmetric tree structure)
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Day 1: Debugging for AddTreeMethod (for the non-symmetric tree structure) -done
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Day 2: Debugging for AddTreeMethod (for the non-symmetric tree structure)
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Day 2: Debugging for AddTreeMethod (for the non-symmetric tree structure) -done
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Day 3: Maximum Parsimony Method - solve the problem w/ # of trees
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Day 4: Maximum Parsimony Method - getting help for Jgrapht type array
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Day 5: Maximum Parsimony Method - finalize
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Day 5: Maximum Parsimony Method -
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*Plan for Maximum Parsimony Method has been changed!
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----
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'''Part IV : Maximum Likelihood'''
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----
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''Week 10 Maximum Parsimony Method''
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----
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Day 1: Debugging AddTree Method & commit the source code
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Day 2: PHYLIP installation & learning how to use it
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Day 3: Practicing PHYLIP with MP/ML/Bootstrap methods
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Day 4: Developing the wrapper for PHYLIP MP method (1) - parser
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Day 5: Developing the wrapper for PHYLIP MP method (2) - builing objects from the output
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'''Part IV : Maximum Likelihood'''
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----
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''Week 10 Maxumum Likelihood Method''
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''Week 11 Maxumum Likelihood Method''
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