I.4 - Agrogenom species phylogeny

Different methods were attempted to estimate the species tree:a) concatenating gene alignements and using RAxML (under a GTRCAT model, 50 rate categories) to infer the tree from the single concatenate: 1) of 455 core unicopy gene families present in all 47 genomes; 2) of 49 unicopy ribosomal gene families present in at least 45/47 genomes;b) using multiple concatenate of a random jackknife sample of genes and inferring a tree with PhyML (under a GTR+G8+I model) for each of them, and then generate the MRE consensus and use split frequency from the sample's trees to infer branch support: 3) from 500 samples of 25 gene families out of the 455 unicopy core families.The reftree/ folder contains the chosen phylogeny, which is based on strategy (3) and further tree annotations such as internal node names.