Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

This data depository contains analysis results from Parks, Wickett, and Alverson 2017 (Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta) (Mol. Biol. Evol. doi:10.1093/molbev/msx268)), and is made freely available to the research community.

The file and subfolders here are as follows:

gene_alignments
- contains compressed (tarred and gzipped) folders with all gene alignments at 0.2, 0.5 and 0.8 alignment column occupancy cutoffs. In each folder, there are also text files listing which gene alignments fall under which taxon occupancy subsetting strategy (i.e., 10-20% taxon occupancy, 40-60% taxon occupancy, 80-100% taxon occupancy, etc).

gene_trees
- contains all (compressed) gene trees (bootstrapped versions, 100 bootstrap pseudo-replicates)) used in Astral analyses for each alignment column occupancy cutoff (0.2, 0.5, 0.8); nodes with less than 33% bootstrap support are collapsed.

hmms.mafft_aligned
- contains (compressed) hmm specifications for each major diatom morphotype (radial and polar centrics, araphid and raphid pennates) from the 0.2 alignment column occupancy subset of the data. A summary of the sampling scheme and the hmm results/counts are also available in HMM_sampling.docx.

mmetsp_nuclear_transcriptome_assemblies
- these are the compressed nuclear transcriptome assemblies that were done in-house (i.e., mostly MMETSP samples). Assemblies do not include organellar or rDNA loci.

species_trees
- contains (compressed) species trees for all phylogenetic strategies and alignment column occupancy cutoff/data subset strategies.

Suppl_1.MMETSP_basic_summaries.xlsx
- this an identical file to Parks, Wickett and Alverson 2017 supplementary file 1. This file contains taxon, strain and SRA information for all assembled taxa, and a variety of assembly metric information.