roblanf/sarscov2phylo: 31-7-20

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