...
| Code Block | ||
|---|---|---|
| ||
InferNetwork_ML (gene_tree_ident1 [, gene_tree_ident2...]) geneTreeList numReticulations [-a taxa map] [-bl] [-b threshold] [-s startingNetwork] [-n numNetReturned] [-h {s1 [,s2...]}] [-w (w1,w2,w3,w4)] [-f maxFailure] [-x numRuns] [-m maxNetExamined] [-d maxDiameter] [-p (rel,abs)] [-r maxRounds] [-t maxTryPerBr] [-i improveThreshold] [-l maxBL] [-pl numProcessors] [-di] [result output file] |
geneTreeList | Comma delimited list of gene _tree_ident1 [, gene_tree_ident2...]Comma delimited list tree identifiers or comma delimited list of sets 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 |
| -bl | Use the branch lengths of the gene trees for the inference. | 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 |
| -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 5. | 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 |
-p (rel, abs) | The original stopping criterion of Brent’s algorithm. Default value is (0.01, 0.001). | optional |
-r maxRound | Maximum number of rounds to optimize branch lengths for a network topology. Default value is 100. | optional |
-t maxTryPerBr | Maximum number of trial per branch in one round to optimize branch lengths for a network topology. Default value is 100. | optional |
-i improveThreshold | Minimum threshold of improvement to continue the next round of optimization of branch lengths. Default value is 0.001. | optional |
-l maxBL | Maximum branch lengths considered. Default value is 6. | 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 |
...