This package provides functions for genearing a genealogy of aligned DNA sequences and extracting properties from it. If there are no recombiations, the genealogy is represented as a coalescent tree, and otherwise it may be represented as an ancestral recombiation graph (ARG) or a list of local trees. The sequences are represented continuously from 0 to 1 if not explictly specified.
RandomARG — generates an ARG.
ARGToLocalTrees — transforms an ARG into a list of genealogical trees at recombination points.
GetLocalTree — gets the local tree at a given position along sequences from an ARG
ResetTreeX — resets the x cordinates of vertices of a tree
ToCoalescentTree — transforms tree format from a graph into a CoalescentTree.
CoalescentTree — represents a data structure for a coalescent tree.
RandomCoalescentTree — generates a CoalescentTree.
ToCombinatoricaGraph — transforms tree format from a CoalescentTree into a CombinatoricaGraph.
SameCoalescentTreeQ — judges whether two trees are same.
SubCoalescentTree — extracts the coalescent tree for a subset of leaves.
TreeTopology — gets the topology of a tree.
TreeToAdjacencyList — gets the adjacency list of a tree.
TreeNodeParent — gets the parent node of a node of a tree.
LeafNumber — gets the number of leaves of a tree.
TotalBranchHeight — gets the total heights of branches of a tree.
BranchHeights — gets a list of branch heights of a tree.
TreeHeight — gets the height of a tree.
TreeCorrelation — gives the correlation coefficient between two trees.
TreeRFDistance — gives the RF distance between two trees.
mSMCRecombination — generates a recombination event on a tree based on the modified Sequential Markov Coalescent (mSMC) model.
mSMCCoalescent — generates the coalescent event of the emerging branch based on the stanadard coalescent without recombation model.
mSMCTransition — generates the mSMC transtion on a tree.
NextLocalTree — gets the tree from a tree and a transition operator.
RandomNextLocalTree — generates a random tree from the current tree after one recombination event, based on the mSMC process.
RandomSequentialTrees — generates local trees along chromosomes based on the mSMC process.
RandomSNPs — generates SNPs by simulating mutations on local trees.
