Description
Infers a species network(s) with a specified number of reticulation nodes under MDC criterion using parsimony-based method. The reticulation nodes in the inferred network will have inferred inheritance probabilities associated with them. To find the optimal network, steepest descent is used. The species network and gene trees must be specified in the Rich Newick Format. However, only topologies of them are used in the method.
Usage
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] [result output file]
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 |
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.
By default, the search terminates when a local optimum is reached. However, option -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.
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.
Examples
#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;
Command References
- Y. Yu, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Under review.
- Y. Yu and L. Nakhleh. Fast algorithms for reconciliation under hybridization and incomplete lineage sorting. Under review.