This archive includes all of the trees (in Newick format) resulting from analyses of the Phylip-formatted data matrices in “Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods” by Lindgren and Anderson. The files are organized into several directories. initial-analyses: This directory includes all of the trees gerneated in our initial set of analyses, as follows: basic_concats: Includes trees resulting from partitioned-by-locus RAxML analyses of the concatenated data matrices for the all, best 1 and best 2 25%, 50% and 75% matrices in the “basic-concats” directory in the “data_files” directory of this archive (see “data_files_readme.txt” and the DetailedMethods.docx file in this archive for more information). For example, “all-25.tre” is the bipartition file resulting from partitioned RAxML analysis of the all 25% data matrix. DOLS: Includes trees resulting from partitioned-by-locus RAxML analyses of the concatenated data matrices for the all, best 1 and best 2 25%, 50% and 75% matrices in the “DOLS-concats” directory in the “data_files” directory of this archive. lopho: These are the trees resulting from partitioned-by-locus RAxML analyses of the concatenated data matrices for the all, best 1 and best 2 50% matrices in the “LCO-concats” directory in the “data_files” directory of this archive. TB: Includes trees resulting from partitioned-by-locus RAxML analyses of the concatenated data matrices for the all, best 1 and best 2 25%, 50% and 75% matrices in the “TB-concats” directory in the “data_files” directory of this archive. MARE: Includes trees resulting from partitioned-by-locus RAxML analyses of the concatenated data matrices for the all, best 1 and best 2 25%, 50% and 75% matrices in the “MARE-concats” directory in the “data_files” directory of this archive. SuskoRoger: Includes trees resulting from unpartitioned RAxML analyses (under the MULTICAT model) of the concatenated data matrices for the all, best 1 and best 2 25%, 50% and 75% matrices in the “SuskoRoger” directory in the “data_files” directory of this archive. PhyloBayes: Includes consensus trees of all post-burn-in trees resulting from PhyloBayes analysis of the best1-75-concat.phy and best2-75-concat.phy files (see “data_files_readme.txt” for details). All PhyloBayes output for these data sets is available by request to FEA. --- Trees based on data sets incorporating data used in Tanner et al. (2017) are organized in three other directories: best1+Grimpoteuthis+Spirula-trees: Includes trees from partitioned-by-locus analyses of unfiltered and TreSpex-and-BaCoCa-filtered 25%, 50% and 75% data matrices in which data for Grimpoteuthis glacialis and Spirula spirula were added to our "best1" set of transcriptomes prior to processing through our pipeline. combined-trees: Includes trees from partitioned-by-locus analyses of matrices from various forms of filtering and recoding of the 25%, 50% and 75% data sets based on the best transcriptomes used in our initial analyses combined with the best transcriptomes used by Tanner et al., 2917; matrices were produced using our cephalopod core ortholog set and (as a check) the prepackaged lophotrochozoan core ortholog set in HaMStR. new-Tanner-trees: Includes trees from partitioned-by-locus analyses of 25%, 50% and 75% matrices for our versions of the Tanner et al. (2017) data set; please see the paper for details.