- _ -

• __init__() : ptreegen.computation.Computation , ptreegen.distance_matrix.DistanceMatrix , ptreegen.parsimony.SmallParsimony , ptreegen.visualization.Visualization , ptreegen.parsimony.LargeParsimony , ptreegen.neighbor_joining.NeighborJoining
• _assign() : ptreegen.parsimony.SmallParsimony
• _solve() : ptreegen.parsimony.SmallParsimony

- a -

• appendData() : ptreegen.distance_matrix.DistanceMatrix

- c -

• checkAlignment() : ptreegen.computation.Computation
• cleanAlignment() : ptreegen.computation.Computation
• columnNames() : ptreegen.distance_matrix.DistanceMatrix
• computeDistanceMatrix() : ptreegen.computation.Computation
• computeTree() : ptreegen.computation.Computation
• cost() : ptreegen.parsimony.SmallParsimony , ptreegen.parsimony.LargeParsimony

- d -

• distMatrix() : ptreegen.distance_matrix.DistanceMatrix

- g -

• getDistance() : ptreegen.distance_matrix.DistanceMatrix
• getIdx() : ptreegen.distance_matrix.DistanceMatrix
• getName() : ptreegen.distance_matrix.DistanceMatrix
• getNearestNeigbors() : ptreegen.distance_matrix.DistanceMatrix
• getOptimalQuartets() : ptreegen.parsimony.LargeParsimony
• getQuartetID() : ptreegen.parsimony.LargeParsimony
• getSeparation() : ptreegen.distance_matrix.DistanceMatrix
• getTopologyID() : ptreegen.parsimony.LargeParsimony

- i -

• increaseCostOnPath() : ptreegen.parsimony.LargeParsimony

- p -

• parseOptions() : ptreegen.computation.Computation , ptreegen.visualization.Visualization
• printToStdout() : ptreegen.visualization.Visualization

- q -

• quartetPuzzling() : ptreegen.parsimony.LargeParsimony

- r -

• removeData() : ptreegen.distance_matrix.DistanceMatrix

- s -

• saveNewick() : ptreegen.visualization.Visualization
• savePNG() : ptreegen.visualization.Visualization
• saveSVG() : ptreegen.visualization.Visualization
• show() : ptreegen.visualization.Visualization
• showGUI() : ptreegen.visualization.Visualization
• showResults() : ptreegen.computation.Computation
• size() : ptreegen.distance_matrix.DistanceMatrix

- t -

• tree() : ptreegen.neighbor_joining.NeighborJoining , ptreegen.parsimony.LargeParsimony
• treeFromQuartet() : ptreegen.parsimony.LargeParsimony

- u -

• update() : ptreegen.computation.Computation