SuperTreeSupport¶
by Tobias Hill, implementing methods by Mark Wilkinson
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class
SuperTreeSupport(supertree, inputTrees)[source]¶ Supertree support measures
Super tree support can be used to calculate a number of support measures for a set of trees and a supertree. The measures can be at split level and placed on the supertree for image production or at tree level with a number of summary measures.
The support of the input trees for a supertree is measured by counting the number of input trees that support(S), conflict(Q), permits(P) or are relevant(R) with the splits in the supertree.
Supply a supertree and the input trees used to create it. Filenames or trees will do. A single supertree and a list of input trees.
For example:
sts = SuperTreeSupport('supertree.nex', 'input.nex')
or:
read('input.nex') inputTrees = var.trees sts = SuperTreeSupport('supertree.nex', inputTrees) sts.doSaveDecoratedTree = True sts.decoratedFilename='mytree.nex' sts.doSaveIndexTree=False sts.indexFilename='mytreeIndex.nex' sts.csvFilename='mytreeIndex.csv' sts.doDrawTree=True sts.verbose=1 sts.superTreeSupport()
After completing the analysis there are a number of placeholders that allows access to the resulting data:
sts.decoratedSuperTree sts.indexSuperTree sts.csvList sts.T, no. of input trees; sts.L, no. of leaves; sts.C, coverage (average proportion of leaves in the input tree); sts.mean, mean taxon overlap among input trees sts.median, median taxon overlap among input trees sts.SC, number of supertree clades; sts.U, no. of unsupported supertree clades; sts.UC, no. of unsupported supertree clades that conflict with at least one input tree; sts.UCC, no. of unsupported clades conflicting with all relevant input trees; sts.QS, average qualitative support for supertree clades. Figures in parentheses are ranges. sts.S, average support sts.P, average permitted sts.Q, average conflict sts.R, average relevance sts.V, average V for supertree clades V = (s minus q)/(s + q) sts.VV, V+ = (s - q + p)/(s + q + p) sts.Vv, V minus = (s - q - p)/(s + q + p) sts.wV, wV = (ws minus q)/(ws + q) sts.wVV, wVV = (ws minus q +wp)/(ws + q + wp) sts.wVv, wVv = (ws minus q minus wp)/(ws + q + wp)
These can be used for further analysis.
Examples of support, conflict, relevance and permission:
Support:
supertree: +--------1:A +--------5:100 | +--------2:B 0 |--------3:C | +--------4:D input tree: +--------1:A +--------5:100 | +--------2:B 0 |--------3:C
Conflict:
supertree: +--------1:A +--------5:100 | +--------2:B 0 |--------3:C | +--------4:D input tree: +--------1:A +--------5:100 | +--------2:C 0 |--------3:B | +--------4:D
Relevance, i.e an input tree split that is irrelevant to the supertree split:
supertree: +--------1:A +--------7:50 | +--------2:B | |--------3:C 0 |--------4:D | |--------5:E | +--------6:F input tree: +--------1:E +--------7:50 | +--------2:F | |--------3:C 0 |--------4:D | |--------5:A
Permission, i.e. an input trees split that permits the supertree split but does not support it:
supertree: +--------1:A +--------7:50 | +--------2:B | |--------3:C 0 |--------4:D | |--------5:E | +--------6:F input tree: +--------1:A +--------7:50 | +--------2:B | | 0 |--------3:C | |--------4:D | |--------5:E
The analysed supertree can be decorated in three different ways.
V = (s minus q)/(s + q) in standard mode, i.e. values between 0 - 100.
V = (s minus q)/(s + q) in supertree mode, i.e. values between -1 - 1
With indices that can be correlated to a csv file holding the support values. This allows for further analysis of the support values and post mapping to the tree.