Biopython upgma树构造没有给出ultrametric树

时间:2016-04-06 20:30:40

标签: bioinformatics biopython

names = ['a', 'b', 'c', 'd', 'e', 'f', 'g']
matrix = [[0.0],
          [0.0187, 0.0],
          [0.0307, 0.0209, 0.0],
          [0.0352, 0.0259, 0.0069, 0.0],
          [0.0346, 0.0242, 0.0075, 0.0065, 0.0],
          [0.0366, 0.0279, 0.0109, 0.0072, 0.0135, 0.0],
          [0.0671, 0.0662, 0.0699, 0.0684, 0.0743, 0.0617, 0.0],
          [0.0471, 0.0384, 0.0212, 0.0149, 0.0209, 0.0122, 0.0645, 0.0]]

distanceMatrix = TreeConstruction._DistanceMatrix(names, matrix)
treeConstructor = TreeConstruction.DistanceTreeConstructor(
    method = 'upgma')
upgmaTree = treeConstructor.upgma(distanceMatrix)
Phylo.draw(upgmaTree)

给出:

Dendrogram

预期(注意分支“g”的长度):

enter image description here

0 个答案:

没有答案