• Infer_ST_MC Command
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Infer the species tree from gene trees using an greedy consensus which can deal with gene trees having multiple alleles in species and unrooted gene trees. The gene trees must be specified in the Rich Newick Format. The generated output trees will also be generated in the rich newick format.


gene_tree_ident1 [, gene_tree_ident2...]

Comma delimited list of gene tree identifiers. See details.



Specifies gene trees should be treated as unrooted.


-a taxa map

Gene tree / species tree taxa association.


result output file

Optional file destination for command output.


By default, it is assumed that gene trees are rooted. However, the option -u can specify gene trees to be treated as unrooted. 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.


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