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Infers the species tree by GLASS. The gene trees must be specified in the rich newick format Rich Newick Format. The generated output trees will also be generated in the rich newick format.
Usage
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infer_ST_stGLASS {(gene_tree_ident1 [, gene_tree_ident2...]}]) [-a taxa map] [result output file] |
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gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited set list of gene tree identifiers. See details. | mandatory]]></ac:plain-text-body></ac:structured-macro> |
-a taxa map | Gene tree / species tree taxa association. | optional |
result output file | Optional file destination for command output. | optional |
Specified gene trees must have branch length. By default, it is assumed that only one individual is sampled per species in gene trees. However, the option -a [ allows multiple alleles to be sampled.
Examples
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#NEXUS BEGIN NETWORKS; Network g1 = ((((a:1,b:2),c:1),d:1),e:2); Network g2 = ((((a:2,b:1),c),d),e); Network g3 = ((((a,b),c),d),e); Network g4 = ((a,b),((c,e),dc:1,e:1),d:2))); Network g5g3 = ((a:1,c:2),((b:1,e:2),d:1)); Network g6 = ((((a,b),c),d),e); Network g7 = ((a,b),((c,e),d)); END; BEGIN PHYLONET; Infer_ST_DVGLASS (g1, g2, g3, g4, g5, g6, g7); END; |
Command References
- Elchanan Mossel and Sebastien Roch. Incomplete lineage sorting: Consistent phylogeny estimation from multiple loci. IEEE/ACM Transactions on Computational
Biology and Bioinformatics, 2008.