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Usage
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networks | Comma delimited list of networks to summarize. | mandatory |
mode | A number in {1,2,3,4,5}. 1: Displayed trees. Each tree is obtained from the network by removing one of the two reticulation edges for each reticulation node. 2: Backbone networks. Each backbone network is obtained by removing one of the two reticulation edges for each node in a subset of the set of all reticulation nodes. 3: Tree decomposition. A network is decomposed at each reticulations. Taxon names cannot include character "*" or "#" in this mode. 4: Tripartition. This tripartition is different from the one in Charnet. X : P1|P2, where X is the set of taxa that are under this reticulation node, and P1 and P2 are two sets of taxa that are under the two siblings of this reticulation node, respectively. 5: Major trees. If the input networks only contain topologies without inheritance probabilities, the user should not use this mode. Each major tree is obtained from the network by removing for each reticulation node the reticulation edge with the lower inheritance probability. | mandatory |
-n | If specified, normalize input networks proportion, make their summation to be 1. Default value is false, which means no normalization. | optional |
-o outputFile | If specified, the output file is outputFile. The default outputFile is SummarizeNetworks.txt under the user's directory. | optional |
Examples
Input networks have proportions.
Download: wheatExample.nex
Please don't copy and paste, since some illegal characters might be copied.
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#NEXUS BEGIN NETWORKS; Network net1=[&W 0.33]((((Ash,(At,TaD)))X#H1,Y#H2),((((Asp,TaB),X#H1),((TaA,Tu),Tm)))Y#H2); Network net2=[&W 0.33]((((Ash,(At,TaD)))X#H1,((Asp,TaB),((((TaA,Tu),Tm),X#H1))Y#H2)),Y#H2); Network net3=[&W 0.2]((((((Ash,(At,TaD)))X#H1,((Asp,TaB))Y#H2),((TaA,Tu),Tm)),X#H1),Y#H2); Network net4=[&W 0.07]((((((Ash,(At,TaD)))X#H1,((Asp,TaB))Y#H2),((TaA,Tu),Tm)),Y#H2),X#H1); Network net5=[&W 0.05]((((Ash,(At,TaD)))X#H1,((Asp,TaB))Y#H2),(((TaA,Tu),Tm),(X#H1,Y#H2))); END; BEGIN PHYLONET; SummarizeNetworks (net1,net2,net3,net4,net5) 2 -n; END; |
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