Tree.txt
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We have prepared a ZIP archive (example_data.zip) which contains our Tree of Life (filename tree_of_life.tree.txt) and various example annotation files, filled mostly with random data. Try uploading the tree, and then dropping some of the annotation files onto it to get an idea how to prepare the annotations for your own trees.
a ZIP archive containing the tree and all other dataset and annotation files. Your tree file must have the extension .tree or .tree.txt. All other files can be named as you wish. When the files are processed during upload, they will be sorted by name, allowing you to order the datasets (if required).
Each gene duplication event is cross-referenced to the species tree node, the orthogroup/gene tree in which it occurred and the node in that gene tree. It also lists the genes descended from each of the two copies arising from the gene duplication event. We can check this out for our FBgn0005648 orthologues. For this we need to look at the gene tree in the Resolved_Gene_Trees/OG0001189_tree.txt. This directory contains the gene trees with the nodes labelled. These files show how OrthoFinder interpreted the gene trees when inferring orthologues and gene duplication events. They can differ slightly from the original gene trees that came directly from the tree inference step (available in Gene_Trees/). To get the Resolved Gene Trees OrthoFinder carries out a Duplication-Loss-Coalescence analysis to identify the more parsimonious interpretation of the tree. 781b155fdc