Gene to species mapping

You need to specify the mappings from gene leaves to species leaves. We currently support three formats (they are auto-detected at runtime). If you want us to support more formats, please open an issue.

Species-genes mapping file

species1:gene1;gene2;gene3
species2:gene4;gene6
species3:gene5

Genes-species mapping file:

gene1 species1
gene2 species1
gene3 species1
gene4 species2
gene6 species2
gene5 species3

Mapping inferred from the taxa names

When no mapping file is given, the mappings are inferred from the gene and species taxa names. The species name should not contain underscores (_) and the gene names should start with the species name followed by an underscore:

species tree:

((species1, species2), species3);

gene tree:

((species1_gene1, species1_gene2), (species1_gene3, (species2_gene4, species3_gene5)), species2_gene6);