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InferNetwork_parsimony (gene_tree_ident1 [, gene_tree_ident2...|, gene_tree_ident2...]) numReticulations [-a taxa map] [-b threshold] [-s startingNetwork] [-n numNetReturned] [-m maxNetExamined] [-d maxDiameter] [-h {s1 [,s2...]}] [-w (w1,w2,w3,w4)] [-f maxFailure] [-x numRuns] [-pl numProcessors] [-di] [result output file]
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gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited list of gene tree identifiers. | mandatory |
numReticulations | Maximum number of reticulations to added. | mandatory |
-b threshold | Gene trees bootstrap threshold. | optional |
-a taxa map | Gene tree / species tree taxa association. | optional |
-s startingNetwork | Specify the network to start search. Default value is the optimal MDC tree. | optional |
-n numNetReturned | Number of optimal networks to return. Default value is 1. | optional |
-m maxNetExamined | Maximum number of network topologies to examined. Default value is infinity. | optional |
-d maxDiameter | Maximum diameter to make an arrangement during network search. Default value is infinity. | optional |
-h {s1 [, s2...]} | A set of specified hybrid species. The size of this set equals the number of reticulation nodes in the inferred network. | optional |
-w (w1, w2, w3, w4) | The weights of operations for network arrangement during the network search. Default value is (0.15, 0.15, 0.2, 0.5). | optional |
-f maxFailure | The maximum number of consecutive failures before the search terminates. Default value is 100. | optional |
-x numRuns | The number of runs of the search. Default value is 10. | optional |
-pl numProcessors | Number of processors if you want the computation to be done in parallel. Default value is 1. | optional |
-di | Output the Rich Newick string of the inferred network that can be read by Dendroscope. | optional |
result output file | Optional file destination for command output. | optional |
It is mandatory to specify the number of reticulation nodes to added to the starting network. The -s option allows the users to specify a starting network (can be a tree) for network search. Then starting from this network, numReticulations number of reticulation nodes will be added during steepest descent search. If the starting network is not specified, the optimal tree under MDC (command inferST_MDC) will be used. If it is not binary, a random resolution will be used. By default, only the first optimal species network will be returned. However, users can use -n option to ask for multiple optimal networks.
Simple hill climbing is used for the search. Users can specify the weights of four operations for network arrangement through option -w. By default, the search terminates when a local optimum is reachedpreset limit of consecutive failures is reached (Default is 100, but users can change it through option -f). However, option -m m allows users to specify the maximum number of networks examined during the search. Once that number is reached, the program will terminate and return the optimal network found so far. On the other hand, users can use option -d to specify the maximum diameter of an operation for network rearrangement, like what local-SPR does. In order to avoid getting stuck at some local optimum, it is recommended to performed the search multiple times, which users can specify by option -x.
By default, it is assumed that only one individual is sampled per species in gene trees. However, the option [-a
taxa map
]
allows multiple alleles to be sampled. If users have a prior knowledge of the hybrid species, they can specify them using option -h.
If users want to run the computation in parallel. Please specify the number of processors through option -pl.
Examples
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#NEXUS BEGIN TREES; Tree geneTree1 = (C,((B,D),A)); Tree geneTree2 = (B,(D,(C,A))); Tree geneTree3 = (D,(B,(C,A))); Tree geneTree4 = (D,(B,(C,A))); END; BEGIN PHYLONET; InferNetwork_parsimony (geneTree1,geneTree2,geneTree3,geneTree4) 1; END; |
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- Y. Yu, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Under review Systematic Biology, vol. 62, no. 5, pp. 738-751, 2013.
- Y. Yu, N. Ristic and L. Nakhleh. Fast algorithms and Heuristics for reconciliation Phylogenomics under hybridization and incomplete lineage sorting. BMC Bioinformatics, vol. 14, no. Under reviewSuppl 15, p. S6, 2013.
- Y. Yu, J. Dong, K. Liu, and L. Nakhleh, Probabilistic inference of reticulate evolutionary histories, Under Review.