Citation Please cite this release as: Lanfear, Rob (2020). A global phylogeny of SARS-CoV-2 from GISAID data, including sequences deposited up to 31-July-2020. Zenodo DOI: 10.5281/zenodo.3958883 You can visit that DOI here: Details The trees in this release were generated with the following command line: bash global_tree_gisaid.sh -i gisaid_hcov-19_2020_07_31_06.fasta -o global.fa -t 27 The raw sequence file contains all available SARS-CoV-2 genomes in GISAID available on the 31st of July 2020, Canberra (Australia) time. The ZIP file contains the code necessary to reproduce the trees themselves, and the README in the zip file also describes the methods used in detail. I also include the trees themselves here so that they can be easily downloaded without downloading the entire repo. Filtering statistics sequences downloaded from GISAID 48019 // alignment stats of global alignment Alignment number: 1 Format: aligned FASTA Number of sequences: 48014 Alignment length: 29903 Total # residues: 1432575924 Smallest: 29030 Largest: 29903 Average length: 29836.6 Average identity: 100% // alignment stats of global alignment after masking sites Alignment number: 1 Format: aligned FASTA Number of sequences: 48014 Alignment length: 29903 Total # residues: 1424431566 Smallest: 28961 Largest: 29675 Average length: 29667.0 Average identity: 100% // alignment stats after filtering out short/ambiguous sequences Alignment number: 1 Format: aligned FASTA Number of sequences: 47815 Alignment length: 29903 Total # residues: 1418538813 Smallest: 29054 Largest: 29675 Average length: 29667.2 Average identity: 100% // alignment stats of global alignment after trimming sites that are >50% gaps Alignment number: 1 Format: aligned FASTA Number of sequences: 47815 Alignment length: 29661 Total # residues: 1415077600 Smallest: 28437 Largest: 29661 Average length: 29594.8 Average identity: 100% // After filtering sequences with TreeShrink Type: Phylogram #nodes: 85486 #leaves: 47779 #dichotomies: 36010 #leaf labels: 47779 #inner labels: 37705 Notable changes to the scripts in this release None Notable aspects of the trees None