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.