Data from: A phylogenomic resolution of the sea urchin tree of life

Echinoidea 70% occupancy matrixContains 331,188 aligned aminoacid positions for 32 taxa, in fasta format. Output by Agalma v. 1.0.1.echinoids70.fa70% matrix without Arbacia punctulataContains 331,188 aligned aminoacid positions for 31 taxa, in fasta format. Same as 'echinoids70.fa' but without Arbacia punctulata. Most analyses in the manuscript were performed using this matrix.echinoids70_noarba.fa70% matrix with decontaminated ArbaciaAll loci in the transcriptome of Arbacia punculata that are identical to those of Eucidaris tribuloides have been deleted in this version of the matrix.echinoids70_nocont_arba.fa70% matrix without Arbacia output by TreeShrinkThis matrix was obtained with TreeShrink which eliminated 345 sequences that behaved as outliers with regards to branch length.echinoids70_noarba_treeshrink.faPartition fileContains the start and end of loci. Output by Agalma v. 1.0.1.echinoids70_partition.txtAll 1,040 gene treesObtained using RAxML v8.2.1 under the model that minimizes the BIC for each loci. Individual gene sequences come from file 'echinoids70_noarba.fa'. Trees are in newick format.all_gene_trees_no_arba.treML phylogeny inferred under mixture model LG4XContains the tree with bootstrap support values in Newick format. Obtained using RAxML-NG v. 0.5.1 using matrix 'echinoids70_noarba.fa'.noarba_unpartitioned_LG4X.raxml.supportML phylogeny inferred under best-fit partitioning schemeContains the tree with bootstrap support values in Newick format. Obtained using RAxML v8.2.1 using matrix 'echinoids70_noarba.fa'. Partitioning obtained using IQ-TREE v1.6.6 using the fast-relaxed clustering algorithm among the top 50% of schemes.RAxML_bipartitions.partitioned_MLML phylogeny inferred under mixture model PMSFContains the tree with bootstrap support values in Newick format. Obtained using IQ-TREE v1.6.6 using matrix 'echinoids70_noarba.fa'.iqtree_echinoids.treefileBayesian phylogeny inferred under best-fit modelContains the consensus tree with posterior probabilities in Newick format. Obtained using ExaBayes v. 1.5 using matrix 'echinoids70_noarba.fa'.ExaBayes.treBayesian phylogeny inferred under CAT-PoissonContains the consensus tree with posterior probabilities in Newick format. Obtained using PhyloBayes-MPI v. 1.8.1 using matrix 'echinoids70_noarba.fa'.echinoidscatpoisson.tre.con.treBayesian phylogeny inferred under CAT-GTRContains the consensus tree with posterior probabilities in Newick format. Obtained using PhyloBayes-MPI v. 1.8.1 using matrix 'echinoids70_noarba.fa'. WARNING: this analysis was run for only 3,000 cycles and did not converge.bpcomp.con.trePhylogeny inferred using coalescent methodContains tree with local posterior probabilities in Newick format. Obtained using ASTRAL-II using trees in file 'all_gene_trees_no_arba.tre'.all_trees_ASTRAL.tre345 gene trees selected for coalescent inferenceSubsampling of 345 gene trees from file 'all_gene_trees.tre' with the lowest branch-length heterogeneity and saturation levels. Individual gene sequences come from file 'echinoids70_noarba.fa'.354trees_for_ASTRAL.trePhylogeny inferred using coalescent method using 345 treesContains tree with local posterior probabilities in Newick format. Obtained using ASTRAL-II using trees in file '354trees_for_ASTRAL.tre'.354trees_ASTRAL.trePhylogenies inferred after pruning by TreeShrinkThe .rar file contains the topologies obtained using matrix 'echinoids70_noarba_treeshrink.fa' with IQ-TREE v1.6.6 (model PMSF), ExaBayes v. 1.5 (automatic model selection) and ASTRAL-II.trees_after_TreeShrink.rarSpecies trees inferred from randomly subsampled gene trees100 species trees obtained using ASTRAL-II, each one inferred from 345 randomly subsampled gene trees from file 'all_gene_trees.tre'.results_astral_randreplicates.treR code and necessary data filesR code to replicate all analyses, as well as data files needed for some of the calculations.Echinoids.rar