Dataset from: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance

<p>This repository contains the datasets, code, and results for:</p> <p>Roberts et al. Resolving marine-freshwater transitions by diatoms through a fog of gene tree discordance.</p> <p>CONTACT INFORMATION:</p> <p>Andrew J. Alverson<br> University of Arkansas<br> aja [at] uark [dot] edu</p> <p>Wade R. Roberts<br> University of Arkansas<br> wader [at] uark [dot] edu</p> <p>TAXON LABEL INFORMATION:</p> <p>Genomes have strain ID before genus_species (e.g., CCMP332_Cyclotella_cryptica)<br> Transcriptomes have genus_species before strain ID (e.g., Cyclotella_nana_AJA048-54)</p> <p><br> DATA AND DIRECTORY OVERVIEW:</p> <p>Voucher images of diatom strains collected:</p> <ul> <li>voucher-images.tgz</li> </ul> <p>OrthoFinder output:</p> <ul> <li>orthofinder.zip</li> </ul> <p>Predicted proteomes and coding sequences for each strain:</p> <ul> <li>proteomes.zip</li> <li>coding-sequences.zip</li> </ul> <p>Workflow for phylogenomic dataset assembly and species tree analyses:</p> <ul> <li>phylogenomic-workflow.html</li> <li>phylogenomic-workflow.md</li> <li>phylogenomic-workflow.pdf</li> </ul> <p>Fasta files, alignments, and gene trees for each ortholog:</p> <ul> <li>datasets.zip</li> </ul> <p>Concatenated alignments, partition models, and estimated species trees:</p> <ul> <li>species-trees.zip</li> <li>species-trees.nexus</li> </ul> <p>Analyses results and code to plot figures:</p> <ul> <li>analyses-and-plots.zip</li> </ul> <p>Additional scripts and miscellaneous files:</p> <ul> <li>scripts-and-misc.zip</li> </ul> <p>Supplemental Materials for publication:</p> <ul> <li>supplemental-materials.zip</li> </ul> <p>&nbsp;</p>