- _ -

• _alignment : ptreegen.neighbor_joining.NeighborJoining , ptreegen.parsimony.SmallParsimony , ptreegen.parsimony.LargeParsimony
• _columnNames : ptreegen.distance_matrix.DistanceMatrix
• _cost : ptreegen.parsimony.SmallParsimony
• _distMatrix : ptreegen.distance_matrix.DistanceMatrix , ptreegen.neighbor_joining.NeighborJoining
• _filePrefix : ptreegen.visualization.Visualization
• _formatingMethods : ptreegen.visualization.Visualization
• _names : ptreegen.neighbor_joining.NeighborJoining
• _optimalQuartets : ptreegen.parsimony.LargeParsimony
• _options : ptreegen.visualization.Visualization
• _qpSteps : ptreegen.parsimony.LargeParsimony
• _sequencesDict : ptreegen.parsimony.LargeParsimony , ptreegen.parsimony.SmallParsimony
• _storageDir : ptreegen.visualization.Visualization
• _style : ptreegen.visualization.Visualization
• _tree : ptreegen.parsimony.LargeParsimony , ptreegen.parsimony.SmallParsimony , ptreegen.visualization.Visualization
• _treeCharacterDict : ptreegen.parsimony.SmallParsimony

- a -

• algorithm : ptreegen.computation.Computation
• alignment : ptreegen.computation.Computation

- d -

• distanceMatrix : ptreegen.computation.Computation
• distFunction : ptreegen.computation.Computation

- g -

• gapCutoff : ptreegen.computation.Computation
• gapPenalty : ptreegen.computation.Computation

- i -

• includeGaps : ptreegen.computation.Computation

- o -

• options : ptreegen.computation.Computation

- p -

• pairCutoff : ptreegen.computation.Computation
• parsIterCnt : ptreegen.computation.Computation

- r -

• removePoor : ptreegen.computation.Computation

- s -

• seqType : ptreegen.computation.Computation

- t -

• tree : ptreegen.computation.Computation

- v -

• visualization : ptreegen.computation.Computation