Algorithm 2: Extending algorithm of the maximum spanning tree T.
Input: the set of mutations Mi contained by sub-clone Si; the ratio of Si is αi,i∈[0,C-1]; the information of alignments(reads related mutations). Output: the maximum spanning treeT.
1.	Initating U-1(φ, φ) and T-1(φ, φ);
2.	for(i=0;i＜C;i+ +){
3.	Vi=Vi-1∪Mi；//extending the set of Viin the undirected graph Ui(Vi，Ei);
4.	Ei=ETi-1∪{the relation of edge between Mi s and between Mi and Vi-1}
5.	Peering the depth of S0-Si-1 from Mi;
6.	Re-computing the weight of new added edges between mutations.
7.	Calling algorithm1 to extend the maximum spanning tree Ti. parameters: undirected weight graph Ui(Vi,Ei); upper maximum spanning tree Ti-1(Vi-1,ETi-1), the number of mutations in Miis ni;
8.	Saving the connection mode between mutations of sub-clone Si, that is, haplotypes;
9.	}
10.	End of algorithm,TC-1(VC-1,ETC-1) is the final extended maximum spanning treeT.