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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] [-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 |
| -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 |
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