09-7-20
The trees in this release were generated with the following command line:
bash global_tree_gisaid.sh -i gisaid_hcov-19_2020_07_09_04.fasta -o global.fa -t 34
The raw sequence file contains all available SARS-CoV-2 genomes in GISAID available on the 9th of July 2020, at 4PM 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
39366
//
alignment stats of global alignment
Alignment number: 1
Format: aligned FASTA
Number of sequences: 38950
Alignment length: 29903
Total # residues: 1162549765
Smallest: 29146
Largest: 29903
Average length: 29847.2
Average identity: 100%
//
alignment stats of global alignment after masking sites
Alignment number: 1
Format: aligned FASTA
Number of sequences: 38950
Alignment length: 29903
Total # residues: 1157204550
Smallest: 29096
Largest: 29718
Average length: 29710.0
Average identity: 100%
//
alignment stats after filtering out short/ambiguous sequences
Alignment number: 1
Format: aligned FASTA
Number of sequences: 38792
Alignment length: 29903
Total # residues: 1152514216
Smallest: 29096
Largest: 29718
Average length: 29710.1
Average identity: 100%
//
alignment stats of global alignment after trimming sites that are >50% gaps
Alignment number: 1
Format: aligned FASTA
Number of sequences: 38792
Alignment length: 29704
Total # residues: 1149590203
Smallest: 28492
Largest: 29704
Average length: 29634.7
Average identity: 100%
//
After filtering sequences with TreeShrink
Type: Phylogram
#nodes: 69583
#leaves: 38699
#dichotomies: 29578
#leaf labels: 38699
#inner labels: 30882
Notable changes to the scripts in this release
- None
Notable aspects of the trees
- None