Pangenome gene trees of 41 Pseudorhizobium and Neorhizobium strains

Gene trees were computed for each of the 6,714 homologous gene family of the 41-species pangenome with at least 4 sequences using MrBayes (Ronquist & Huelsenbeck 2003) under the GTR+4G+I model, running the Metropolis-coupled Markov chain Monte-Carlo (MCMCMC) for 2,000,000 generations, sampling a tree every 500 generations. Convergence of bipartition distribution in independent pairs of 4,000 sampled gene tree sets (‘chains’) was achieved for all gene families under these conditions.
Only the consensus of these tree chains (discarding the first 25% sampled trees as burn-in) are presented here.Correspondance of gene family and coding sequence identifiers with metadata (genome of origin, genome location, functional annotation, etc.) is available using the Pantagruel database provided in the related post (open with SQLite 3).