Stramenopile dataset for positive selection

This repository contains the data (sequences, annotations, and intermediary files) collected and produced during the preparation of the following preprint: https://doi.org/10.1101/2021.01.12.426341. Description of files:

• The samples.zip file contains for each taxa:
  • The functional annotations from Interproscan with extension ".tsv" in a TSV format.
  • The genome annotations with extension ".gff" in a gff3 format.
  • The protein sequences with extension ".faa" in a fasta format.
  • The corresponding coding DNA sequences with extension ".fna" in a fasta format.
• The all_ann.csv file contains all annotations from the tested genes with added information for positive selection and orthology status in a CSV format.
• The go_mapping.csv file contains the mapping of GO terms to protein accessions of the dataset in a CSV format.
• The protein_families.poff.tsv contains the proteinortho output file corresponding to the classification of the genes in the dataset into ortholog groups in a TSV format.
• The families.zip file contains the intermediary files for each of the selected orthogroups:
  • Tree files in newick format in the folder "trees".
  • Protein sequences in the folder  "faas".
  • Coding DNA sequences in the folder "fnas".
  • Log outputs from the FUBAR analysis in the folder "logs".
  • Codon alignments in the folder "codon_alns"
• The families_fubar.zip file contains the same files as before for the subset of orthogroups with a positive result in the FUBAR analysis plus log output from the aBSREL analysis in the log folder.