lingpy.thirdparty package

Subpackages

• lingpy.thirdparty.cogent package
  • Submodules
  • lingpy.thirdparty.cogent.newick module
    • TreeParseError
    • parse_string()
  • lingpy.thirdparty.cogent.tree module
    • LoadTree()
    • PhyloNode
      • PhyloNode.Length
      • PhyloNode.balanced()
      • PhyloNode.bifurcating()
      • PhyloNode.compareByPartitions()
      • PhyloNode.distance()
      • PhyloNode.getDistances()
      • PhyloNode.getNewick()
      • PhyloNode.prune()
      • PhyloNode.rootAtMidpoint()
      • PhyloNode.rootedAt()
      • PhyloNode.rootedWithTip()
      • PhyloNode.sameTopology()
      • PhyloNode.scaleBranchLengths()
      • PhyloNode.setTipDistances()
      • PhyloNode.tipToTipDistances()
      • PhyloNode.totalDescendingBranchLength()
      • PhyloNode.unrooted()
      • PhyloNode.unrootedDeepcopy()
    • TreeBuilder
      • TreeBuilder.createEdge()
      • TreeBuilder.edgeFromEdge()
    • TreeError
    • TreeNode
      • TreeNode.Parent
      • TreeNode.ancestors()
      • TreeNode.append()
      • TreeNode.asciiArt()
      • TreeNode.childGroups()
      • TreeNode.compareByNames()
      • TreeNode.compareBySubsets()
      • TreeNode.compareName()
      • TreeNode.copy()
      • TreeNode.copyRecursive()
      • TreeNode.copyTopology()
      • TreeNode.deepcopy()
      • TreeNode.descendantArray()
      • TreeNode.extend()
      • TreeNode.getConnectingEdges()
      • TreeNode.getConnectingNode()
      • TreeNode.getDistances()
      • TreeNode.getEdgeNames()
      • TreeNode.getEdgeVector()
      • TreeNode.getMaxTipTipDistance()
      • TreeNode.getNewick()
      • TreeNode.getNewickRecursive()
      • TreeNode.getNodeMatchingName()
      • TreeNode.getNodeNames()
      • TreeNode.getNodesDict()
      • TreeNode.getParamValue()
      • TreeNode.getSubTree()
      • TreeNode.getTipNames()
      • TreeNode.get_LCA()
      • TreeNode.indexInParent()
      • TreeNode.insert()
      • TreeNode.isRoot()
      • TreeNode.isTip()
      • TreeNode.isroot()
      • TreeNode.istip()
      • TreeNode.iterNontips()
      • TreeNode.iterTips()
      • TreeNode.lastCommonAncestor()
      • TreeNode.lca()
      • TreeNode.levelorder()
      • TreeNode.lowestCommonAncestor()
      • TreeNode.makeTreeArray()
      • TreeNode.maxTipTipDistance()
      • TreeNode.nameUnnamedNodes()
      • TreeNode.nonTipChildren()
      • TreeNode.nontips()
      • TreeNode.pop()
      • TreeNode.postorder()
      • TreeNode.pre_and_postorder()
      • TreeNode.preorder()
      • TreeNode.prune()
      • TreeNode.reassignNames()
      • TreeNode.remove()
      • TreeNode.removeNode()
      • TreeNode.root()
      • TreeNode.sameShape()
      • TreeNode.separation()
      • TreeNode.setMaxTipTipDistance()
      • TreeNode.setParamValue()
      • TreeNode.siblings()
      • TreeNode.sorted()
      • TreeNode.subset()
      • TreeNode.subsets()
      • TreeNode.tipChildren()
      • TreeNode.tips()
      • TreeNode.traverse()
      • TreeNode.traverse_recursive()
      • TreeNode.writeToFile()
    • cmp()
    • comb()
  • Module contents
• lingpy.thirdparty.linkcomm package
  • Submodules
  • lingpy.thirdparty.linkcomm.link_clustering module
    • Dc()
    • HLC
      • HLC.initialize_edges()
      • HLC.merge_comms()
      • HLC.single_linkage()
    • similarities_unweighted()
    • similarities_weighted()
    • swap()
  • Module contents

Module contents