This archive includes all of the relaxed-Phylip-formatted data matrices and partition files used 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_analyaes: This directory includes all of the data sets used in our initial set of analyses, in six subdirectories. The first five described below contain data/matrices generated using our cephalopod core ortholog set in HaMStR; see manuscript for details.

basic-concats: Includes concatenated data matrices and partition files for the all, best1 and best2 25%, 50% and 75% data sets described in the manuscript. The data matrices were produced by sorting HaMStR output into orthogroups, aligning the orthogroups, and removing putative paralogs using PhyloTreePruner (the methods are summarized in the manuscript). The matrices are named “X-Y-concat.phy”, where “X” represents “all”, “best 1” or “best 2” and Y represents the percentage of transcriptomes in which an orthogroup must be represented to be retained, as described in the manuscript. The partition files used in partitioned-by-OG RAxML analyses use a similar convention, but end with “parts.txt”. These conventions are also used in the directories described below.

TB-concats: As described for basic-concats, but subjected to further filtering using TreSpEx.v.1.1 and BaCoCa v. 1.104r, as described in the manuscript.

DOLS-concats: As described for basic-concats, but the data matrices comprise only loci that 1) include data for at least two representatives of Decapodiformes, Octopus, Myopsida or Sepiida and 2) returned single-gene RAxML trees that contained monophyletic Decapodiformes, Octopodiformes, Myopsida and Sepiida.

MARE-concats: As described for basic-concats, but the data matrices were filtered with MARE v. 0.1.2 as described in the manuscript.

lopho-concats: As described for basic-concats, but these data sets were generated using the lophotrochozoan core ortholog set that comes packaged with HaMStR.

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Data sets incorporating data used in Tanner et al. (2017) are organized as follows:

best1+Grimpoteuthis+Spirula-data: Includes 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-data: Includes 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-data: Includes 25%, 50% and 75% matrices for our versions of the Tanner et al. (2017) data set; please see the paper for details.