Fig. 2

The OrthoFinder workflow. The method used for each step is shown by the arrow. Published algorithms are shown in italics and are followed by an asterisk. A dotted blue line connecting with a solid arrow indicates additional data that are used in order to carry out the transformation indicated by the solid arrow. MSA, multiple sequence alignment-based tree inference; DLC, duplication-loss-coalescence. (a) Orthogroup inference using the original OrthoFinder algorithm (an orthogroup is the set of genes descended from a single gene in the last common ancestor of all the species under consideration). (b) Gene tree inference. (c) Species tree inference. (d) Species tree rooting (e) Gene tree rooting (f) Hybrid overlap + DLC analysis of rooted gene trees to infer orthologs and gene duplication events. (g) Illustration of the ortholog results table for the genes in each input species (four main boxes). The horizontal divisions within these show the orthologs for each individual species pair. (h) Illustration of the gene duplication event table showing the location of the gene duplication events mapped to the species tree, the location in the gene tree, the percent retention of the duplicate genes in the sampled species, and the genes descended from the gene duplication event. (i) Comparative genomics statistics