Genealogy
Chaozhi Zheng
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.
ARG
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.
    
Coalescent Tree
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.
    
Local 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.