Here is a list of all documented files with brief descriptions:

[detail level 12]

▼ SequenceScores
LikelihoodScores.cs
ParsimonyScore.cs
▼ SequenceSimulation
IndelModel.cs
RateMatix.cs
RateMatrices.cs
Sequence.cs
SequenceSimulation.cs
SequenceSimulation.public.cs
▼ TreeBuilding
BirthDeathTree.cs
CoalescentTree.cs
DistanceMatrix.cs
DistanceMatrix.DNA.cs
DistanceMatrix.Protein.cs
MatrixExponential.cs
NeighborJoining.cs
RandomTree.cs
ThreadSafeRandom.cs
UPGMA.cs
AttributeDictionary.cs
Binary.cs
Extensions.cs
NcbiAsnBer.cs
NcbiAsnText.cs
NEXUS.cs
NWKA.cs
TreeCollection.cs
TreeNode.Comparisons.cs
TreeNode.cs
TreeNode.ShapeIndices.cs