Are these available online somewhere? I've written up some code to build phylogenetic trees and infer ancestral sequences. I'd like to try them out on real-world data.
•
written
by
offbynull •
Perhaps download the genomes from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/?term=txid2697049[Organism:noexp]) and use a tool like Biopython to extract the Spike region. Otherwise you need to make an account with GISAID if eligible, be accepted, then you can directly download alignments of the Spike region (nucleotide or amino acid).
Sorry I'm not too familiar with NCBI's interface. Is there a way to download these ~2 million sequences (or some subset) in bulk or do I have to make a script to download each FASTA individually??
The suggestion from GenoMax above is the easiest way. Go here: https://www.ncbi.nlm.nih.gov/datasets/coronavirus/proteins/ then tick the S gene, click download.
Log in to answer this question.
Easier to download the proteins from NCBI datasets page for SARS-CoV-2. Entire genomes available from this page.