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
University of Arkansas
aja [at] uark [dot] edu

Wade R. Roberts
University of Arkansas
wader [at] uark [dot] edu

TAXON LABEL INFORMATION:

Genomes have strain ID before genus_species (e.g., CCMP332_Cyclotella_cryptica)
Transcriptomes have genus_species before strain ID (e.g., Cyclotella_nana_AJA048-54)

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