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

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