| CPU | x86-64 (e.g. Intel Core i3/i5/i7 series) |
| RAM | 8 GB or above |
| OS | 64-bit Linux or macOS |
| Package name | Version | Site URL |
|---|---|---|
| Perl | 5.8 or later | https://www.perl.org (Preinstalled in OS) |
| BEDTools | 2.29.2 | https://github.com/arq5x/bedtools2 |
| NCBI-BLAST+ | 2.2.29 | http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+ |
| FATE | 2.8.0 | https://github.com/Hikoyu/FATE |
| FAMSA | 1.5.12 | https://github.com/refresh-bio/FAMSA |
| ModelTest-NG | 0.1.6 | https://github.com/ddarriba/modeltest |
| RAxML-NG | 0.9.0 | https://github.com/amkozlov/raxml-ng |
Above softwares must be installed and in your PATH. Some softwares need to be compiled. (e.g. BEDTools) For Linux users, 'modeltest-ng', including binary distribution, may cause a segmentation fault error when parallel execution is enabled. Consider using 'modeltest-mpi' as 'modeltest-ng' in stead (or set a shell variable 'num_threads' to 1).
Clone this repository and remove old data before re-analysis. Then, simply execute 'script/all-in-one_analysis.sh' in the top of the repository.
$ git clone https://github.com/Hikoyu/SARS-CoV-2
$ cd SARS-CoV-2
$ rm ref/*.orf.f?a genome/*.fna.* fate/*.bed famsa/*.fna phylogeny/*.* phylogeny/*/DNA/*/*/*.* phylogeny/*/AA/*/*.*
$ ./script/all-in-one_analysis.sh
Now, you can get the multiple sequence alignments of open reading frames, the lists of variable/parsimony-informative sites, and the maximum-likelihood phylogenies. If you want to re-analyze only estimating phylogeny, remove old phylogenetic analysis data and execute 'script/phylogenetic_analysis.sh' in the top of the repository.
$ git clone https://github.com/Hikoyu/SARS-CoV-2
$ cd SARS-CoV-2
$ rm phylogeny/*.* phylogeny/*/DNA/*/*/*.* phylogeny/*/AA/*/*.*
$ ./script/phylogenetic_analysis.sh
Now, you can get the maximum-likelihood phylogenies.
Phylogenetic analyses take a lot of time.
They took over 2 weeks in total on my Linux workstation (4C/8T Intel Xeon E3-1240L v3, 16 GB RAM).
More CPU cores and/or newer streaming SIMD extensions may contribute to reduce the calculation time.
If you intend to just test, reduce the bootstraps replicates to 100 via 'bootstraps_replicates' shell variable in script/phylogenetic_analysis.sh.
| Data format | File extension | Description |
|---|---|---|
| FASTA (DNA) | *.fna | DNA sequence file |
| FASTA (AA) | *.faa | AA sequence file |
| FASTA index | *.fai | fasta index file |
| BED | *.bed | annotation data file |
| Newick | *.nwk | phylogenetic tree file |
SARS-CoV-2
├── README.md
├── famsa => including open reading frame sequence data and multiple sequence alignment data
│ ├── SARS-CoV-2_200414.E.aln.fna
│ ├── SARS-CoV-2_200414.E.fna
│ ├── SARS-CoV-2_200414.M.aln.fna
│ ├── SARS-CoV-2_200414.M.fna
│ ├── SARS-CoV-2_200414.N.aln.fna
│ ├── SARS-CoV-2_200414.N.fna
│ ├── SARS-CoV-2_200414.ORF10.aln.fna
│ ├── SARS-CoV-2_200414.ORF10.fna
│ ├── SARS-CoV-2_200414.ORF3a.aln.fna
│ ├── SARS-CoV-2_200414.ORF3a.fna
│ ├── SARS-CoV-2_200414.ORF6.aln.fna
│ ├── SARS-CoV-2_200414.ORF6.fna
│ ├── SARS-CoV-2_200414.ORF7a.aln.fna
│ ├── SARS-CoV-2_200414.ORF7a.fna
│ ├── SARS-CoV-2_200414.ORF8.aln.fna
│ ├── SARS-CoV-2_200414.ORF8.fna
│ ├── SARS-CoV-2_200414.S.aln.fna
│ ├── SARS-CoV-2_200414.S.fna
│ ├── SARS-CoV-2_200414.orf1ab_D.aln.fna
│ ├── SARS-CoV-2_200414.orf1ab_D.fna
│ ├── SARS-CoV-2_200414.orf1ab_U.aln.fna
│ ├── SARS-CoV-2_200414.orf1ab_U.fna
│ ├── msa_list.txt
│ ├── parsimony-informative_site_position_list.txt
│ ├── parsimony-informative_sites.txt
│ ├── variable_site_position_list.txt
│ └── variable_sites.txt
├── fate
│ └── SARS-CoV-2_200414.orf.bed => open reading frame annotation data
├── genome => including SARS-CoV-2 genome sequence data
│ ├── SARS-CoV-2_200414.fna
│ ├── SARS-CoV-2_200414.fna.fai
│ ├── SARS-CoV-2_200414.fna.nhr
│ ├── SARS-CoV-2_200414.fna.nin
│ ├── SARS-CoV-2_200414.fna.nsq
│ └── sample_list.txt
├── phylogeny
│ ├── ModelTest-NG
│ │ ├── AA
│ │ └── DNA
│ │ ├── part
│ │ │ ├── 3rd => including model test data using partitioned model for each ORF and also 1st/2nd and 3rd codon position
│ │ │ │ ├── SARS-CoV-2_200414.ckp
│ │ │ │ ├── SARS-CoV-2_200414.log
│ │ │ │ ├── SARS-CoV-2_200414.out
│ │ │ │ ├── SARS-CoV-2_200414.part.aic
│ │ │ │ ├── SARS-CoV-2_200414.part.aicc
│ │ │ │ ├── SARS-CoV-2_200414.part.bic
│ │ │ │ ├── SARS-CoV-2_200414.part.txt
│ │ │ │ └── SARS-CoV-2_200414.tree
│ │ │ ├── sep => including phylogenetic analysis data using partitioned model for each ORF and also each codon position
│ │ │ │ ├── SARS-CoV-2_200414.ckp
│ │ │ │ ├── SARS-CoV-2_200414.log
│ │ │ │ ├── SARS-CoV-2_200414.out
│ │ │ │ ├── SARS-CoV-2_200414.part.aic
│ │ │ │ ├── SARS-CoV-2_200414.part.aicc
│ │ │ │ ├── SARS-CoV-2_200414.part.bic
│ │ │ │ ├── SARS-CoV-2_200414.part.txt
│ │ │ │ └── SARS-CoV-2_200414.tree
│ │ │ └── uni => including model test data using partitioned model for each ORF
│ │ │ ├── SARS-CoV-2_200414.ckp
│ │ │ ├── SARS-CoV-2_200414.log
│ │ │ ├── SARS-CoV-2_200414.out
│ │ │ ├── SARS-CoV-2_200414.part.aic
│ │ │ ├── SARS-CoV-2_200414.part.aicc
│ │ │ ├── SARS-CoV-2_200414.part.bic
│ │ │ ├── SARS-CoV-2_200414.part.txt
│ │ │ └── SARS-CoV-2_200414.tree
│ │ └── univ
│ │ ├── 3rd => including model test data using partitioned model for each ORF and also 1st/2nd and 3rd codon position
│ │ │ ├── SARS-CoV-2_200414.ckp
│ │ │ ├── SARS-CoV-2_200414.log
│ │ │ ├── SARS-CoV-2_200414.out
│ │ │ ├── SARS-CoV-2_200414.part.aic
│ │ │ ├── SARS-CoV-2_200414.part.aicc
│ │ │ ├── SARS-CoV-2_200414.part.bic
│ │ │ ├── SARS-CoV-2_200414.part.txt
│ │ │ └── SARS-CoV-2_200414.tree
│ │ ├── sep => including model test data using partitioned model for each codon position
│ │ │ ├── SARS-CoV-2_200414.ckp
│ │ │ ├── SARS-CoV-2_200414.log
│ │ │ ├── SARS-CoV-2_200414.out
│ │ │ ├── SARS-CoV-2_200414.part.aic
│ │ │ ├── SARS-CoV-2_200414.part.aicc
│ │ │ ├── SARS-CoV-2_200414.part.bic
│ │ │ ├── SARS-CoV-2_200414.part.txt
│ │ │ └── SARS-CoV-2_200414.tree
│ │ └── uni => including model test data without using partitioned model
│ │ ├── SARS-CoV-2_200414.ckp
│ │ ├── SARS-CoV-2_200414.log
│ │ ├── SARS-CoV-2_200414.out
│ │ └── SARS-CoV-2_200414.tree
│ ├── RAxML-NG
│ │ ├── AA
│ │ └── DNA
│ │ ├── part
│ │ │ ├── 3rd => including phylogenetic analysis data using partitioned model for each ORF and also 1st/2nd and 3rd codon position
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.0.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.1.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.10.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.11.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.2.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.3.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.4.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.5.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.6.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.7.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.8.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.9.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bsconverge.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.parse.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.raxml.rba
│ │ │ │ ├── SARS-CoV-2_200414.raxml.reduced.partition
│ │ │ │ ├── SARS-CoV-2_200414.raxml.reduced.phy
│ │ │ │ ├── SARS-CoV-2_200414.raxml.support.nwk => maximum-likelihood phylogeny data with bootstrap values
│ │ │ │ ├── SARS-CoV-2_200414.search.0.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.1.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.10.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.11.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.2.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.3.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.4.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.5.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.6.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.7.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.8.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.9.raxml.log
│ │ │ │ └── SARS-CoV-2_200414.support.raxml.log
│ │ │ ├── sep => including phylogenetic analysis data using partitioned model for each ORF and also each codon position
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.0.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.1.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.10.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.11.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.2.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.3.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.4.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.5.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.6.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.7.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.8.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.bestModel
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.bestTree
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.mlTrees
│ │ │ │ ├── SARS-CoV-2_200414.9.raxml.startTree
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.0.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.1.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.10.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.11.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.2.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.3.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.4.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.5.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.6.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.7.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.8.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bootstrap.9.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.bsconverge.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.parse.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.raxml.bootstraps
│ │ │ │ ├── SARS-CoV-2_200414.raxml.rba
│ │ │ │ ├── SARS-CoV-2_200414.raxml.reduced.partition
│ │ │ │ ├── SARS-CoV-2_200414.raxml.reduced.phy
│ │ │ │ ├── SARS-CoV-2_200414.raxml.support.nwk => maximum-likelihood phylogeny data with bootstrap values
│ │ │ │ ├── SARS-CoV-2_200414.search.0.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.1.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.10.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.11.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.2.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.3.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.4.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.5.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.6.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.7.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.8.raxml.log
│ │ │ │ ├── SARS-CoV-2_200414.search.9.raxml.log
│ │ │ │ └── SARS-CoV-2_200414.support.raxml.log
│ │ │ └── uni => including phylogenetic analysis data using partitioned model for each ORF
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.0.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.0.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.1.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.1.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.10.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.10.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.11.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.11.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.2.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.2.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.3.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.3.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.4.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.4.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.5.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.5.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.6.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.6.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.7.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.7.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.8.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.8.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.9.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.9.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.bootstrap.0.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.1.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.10.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.11.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.2.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.3.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.4.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.5.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.6.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.7.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.8.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.9.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bsconverge.raxml.log
│ │ │ ├── SARS-CoV-2_200414.parse.raxml.log
│ │ │ ├── SARS-CoV-2_200414.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.raxml.rba
│ │ │ ├── SARS-CoV-2_200414.raxml.reduced.partition
│ │ │ ├── SARS-CoV-2_200414.raxml.reduced.phy
│ │ │ ├── SARS-CoV-2_200414.raxml.support.nwk => maximum-likelihood phylogeny data with bootstrap values
│ │ │ ├── SARS-CoV-2_200414.search.0.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.1.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.10.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.11.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.2.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.3.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.4.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.5.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.6.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.7.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.8.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.9.raxml.log
│ │ │ └── SARS-CoV-2_200414.support.raxml.log
│ │ └── univ
│ │ ├── 3rd => including phylogenetic analysis data using partitioned model for 1st/2nd and 3rd codon position
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.0.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.0.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.1.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.1.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.10.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.10.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.11.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.11.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.2.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.2.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.3.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.3.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.4.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.4.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.5.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.5.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.6.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.6.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.7.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.7.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.8.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.8.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.9.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.9.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.bootstrap.0.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.1.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.10.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.11.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.2.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.3.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.4.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.5.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.6.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.7.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.8.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.9.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bsconverge.raxml.log
│ │ │ ├── SARS-CoV-2_200414.parse.raxml.log
│ │ │ ├── SARS-CoV-2_200414.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.raxml.rba
│ │ │ ├── SARS-CoV-2_200414.raxml.reduced.partition
│ │ │ ├── SARS-CoV-2_200414.raxml.reduced.phy
│ │ │ ├── SARS-CoV-2_200414.raxml.support.nwk => maximum-likelihood phylogeny data with bootstrap values
│ │ │ ├── SARS-CoV-2_200414.search.0.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.1.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.10.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.11.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.2.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.3.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.4.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.5.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.6.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.7.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.8.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.9.raxml.log
│ │ │ └── SARS-CoV-2_200414.support.raxml.log
│ │ ├── sep => including phylogenetic analysis data using partitioned model for each codon position
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.0.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.0.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.0.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.1.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.1.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.1.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.10.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.10.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.10.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.11.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.11.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.11.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.2.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.2.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.2.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.3.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.3.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.3.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.4.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.4.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.4.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.5.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.5.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.5.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.6.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.6.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.6.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.7.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.7.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.7.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.8.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.8.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.8.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bestModel
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bestTree
│ │ │ ├── SARS-CoV-2_200414.9.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.9.raxml.mlTrees
│ │ │ ├── SARS-CoV-2_200414.9.raxml.startTree
│ │ │ ├── SARS-CoV-2_200414.bootstrap.0.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.1.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.10.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.11.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.2.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.3.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.4.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.5.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.6.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.7.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.8.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bootstrap.9.raxml.log
│ │ │ ├── SARS-CoV-2_200414.bsconverge.raxml.log
│ │ │ ├── SARS-CoV-2_200414.parse.raxml.log
│ │ │ ├── SARS-CoV-2_200414.raxml.bootstraps
│ │ │ ├── SARS-CoV-2_200414.raxml.rba
│ │ │ ├── SARS-CoV-2_200414.raxml.reduced.partition
│ │ │ ├── SARS-CoV-2_200414.raxml.reduced.phy
│ │ │ ├── SARS-CoV-2_200414.raxml.support.nwk => maximum-likelihood phylogeny data with bootstrap values
│ │ │ ├── SARS-CoV-2_200414.search.0.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.1.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.10.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.11.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.2.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.3.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.4.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.5.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.6.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.7.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.8.raxml.log
│ │ │ ├── SARS-CoV-2_200414.search.9.raxml.log
│ │ │ └── SARS-CoV-2_200414.support.raxml.log
│ │ └── uni => including phylogenetic analysis data without using partitioned model
│ │ ├── SARS-CoV-2_200414.0.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.0.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.0.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.0.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.0.raxml.startTree
│ │ ├── SARS-CoV-2_200414.1.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.1.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.1.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.1.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.1.raxml.startTree
│ │ ├── SARS-CoV-2_200414.10.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.10.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.10.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.10.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.10.raxml.startTree
│ │ ├── SARS-CoV-2_200414.11.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.11.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.11.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.11.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.11.raxml.startTree
│ │ ├── SARS-CoV-2_200414.2.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.2.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.2.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.2.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.2.raxml.startTree
│ │ ├── SARS-CoV-2_200414.3.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.3.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.3.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.3.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.3.raxml.startTree
│ │ ├── SARS-CoV-2_200414.4.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.4.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.4.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.4.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.4.raxml.startTree
│ │ ├── SARS-CoV-2_200414.5.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.5.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.5.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.5.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.5.raxml.startTree
│ │ ├── SARS-CoV-2_200414.6.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.6.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.6.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.6.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.6.raxml.startTree
│ │ ├── SARS-CoV-2_200414.7.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.7.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.7.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.7.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.7.raxml.startTree
│ │ ├── SARS-CoV-2_200414.8.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.8.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.8.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.8.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.8.raxml.startTree
│ │ ├── SARS-CoV-2_200414.9.raxml.bestModel
│ │ ├── SARS-CoV-2_200414.9.raxml.bestTree
│ │ ├── SARS-CoV-2_200414.9.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.9.raxml.mlTrees
│ │ ├── SARS-CoV-2_200414.9.raxml.startTree
│ │ ├── SARS-CoV-2_200414.bootstrap.0.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.1.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.10.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.11.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.2.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.3.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.4.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.5.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.6.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.7.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.8.raxml.log
│ │ ├── SARS-CoV-2_200414.bootstrap.9.raxml.log
│ │ ├── SARS-CoV-2_200414.bsconverge.raxml.log
│ │ ├── SARS-CoV-2_200414.parse.raxml.log
│ │ ├── SARS-CoV-2_200414.raxml.bootstraps
│ │ ├── SARS-CoV-2_200414.raxml.rba
│ │ ├── SARS-CoV-2_200414.raxml.reduced.phy
│ │ ├── SARS-CoV-2_200414.raxml.support.nwk => maximum-likelihood phylogeny data with bootstrap values
│ │ ├── SARS-CoV-2_200414.search.0.raxml.log
│ │ ├── SARS-CoV-2_200414.search.1.raxml.log
│ │ ├── SARS-CoV-2_200414.search.10.raxml.log
│ │ ├── SARS-CoV-2_200414.search.11.raxml.log
│ │ ├── SARS-CoV-2_200414.search.2.raxml.log
│ │ ├── SARS-CoV-2_200414.search.3.raxml.log
│ │ ├── SARS-CoV-2_200414.search.4.raxml.log
│ │ ├── SARS-CoV-2_200414.search.5.raxml.log
│ │ ├── SARS-CoV-2_200414.search.6.raxml.log
│ │ ├── SARS-CoV-2_200414.search.7.raxml.log
│ │ ├── SARS-CoV-2_200414.search.8.raxml.log
│ │ ├── SARS-CoV-2_200414.search.9.raxml.log
│ │ └── SARS-CoV-2_200414.support.raxml.log
│ ├── SARS-CoV-2_200414.aln.concat.faa
│ └── SARS-CoV-2_200414.aln.concat.fna
├── ref => including reference open reading frame annotation data
│ ├── MN908947.orf.bed
│ ├── MN908947.orf.faa
│ └── MN908947.orf.fna
└── script
├── LICENSE
├── all-in-one_analysis.sh
├── codon_based_msa.pl
├── parallel_phylogeny.pl
├── phylogenetic_analysis.sh
├── translator.pl
└── variable_sites_extractor.pl
| Accession No. | Database name | Collection date | Country | State/City | Notes |
|---|---|---|---|---|---|
| LC534419 | Genbank | 09-Mar-2020 | Japan | Kanagawa | |
| LC534418 | Genbank | 14-Feb-2020 | Japan | Kanagawa | Diamond Princess cruise ship? |
| LC528233 | Genbank | 10-Feb-2020 | Japan | Kanagawa | Diamond Princess cruise ship? |
| LC528232 | Genbank | 10-Feb-2020 | Japan | Kanagawa | Diamond Princess cruise ship? |
| LC529905 | Genbank | Jan-2020 | Japan | Tokyo | |
| MT308700 | Genbank | 12-Mar-2020 | USA | Michigan | |
| MT308699 | Genbank | 12-Mar-2020 | USA | Michigan | |
| MT308698 | Genbank | 12-Mar-2020 | USA | Michigan | |
| MT308697 | Genbank | 11-Mar-2020 | USA | Michigan | |
| MT308696 | Genbank | 09-Mar-2020 | USA | Michigan | |
| MT308695 | Genbank | 10-Mar-2020 | USA | Michigan | |
| MT308694 | Genbank | 11-Mar-2020 | USA | Michigan | |
| MT308693 | Genbank | 10-Mar-2020 | USA | Michigan | |
| MT308692 | Genbank | 09-Mar-2020 | USA | Michigan | |
| MT308704 | Genbank | Apr-2020 | USA | North Carolina | |
| MT308703 | Genbank | Apr-2020 | USA | North Carolina | |
| MT308702 | Genbank | Apr-2020 | USA | North Carolina | |
| MT304491 | Genbank | 01-Mar-2020 | USA | Texas | |
| MT304490 | Genbank | 01-Mar-2020 | USA | Texas | |
| MT304489 | Genbank | 29-Feb-2020 | USA | Texas | |
| MT304488 | Genbank | 01-Mar-2020 | USA | Rhode Island | |
| MT304487 | Genbank | 01-Mar-2020 | USA | Oregon | |
| MT304486 | Genbank | 02-Mar-2020 | USA | New York | |
| MT304485 | Genbank | 02-Mar-2020 | USA | New Hampshire | |
| MT304484 | Genbank | 29-Feb-2020 | USA | New Hampshire | |
| MT304483 | Genbank | 01-Mar-2020 | USA | Illinois | |
| MT304482 | Genbank | 01-Mar-2020 | USA | Illinois | |
| MT304481 | Genbank | 04-Mar-2020 | USA | Georgia | |
| MT304480 | Genbank | 03-Mar-2020 | USA | Georgia | |
| MT304479 | Genbank | 03-Mar-2020 | USA | Georgia | |
| MT304478 | Genbank | 02-Mar-2020 | USA | Florida | |
| MT304477 | Genbank | 02-Mar-2020 | USA | Arizona | |
| MT304476 | Genbank | 29-Feb-2020 | South Korea | ||
| MT304475 | Genbank | 29-Feb-2020 | South Korea | ||
| MT304474 | Genbank | 27-Feb-2020 | South Korea | ||
| MT281577 | Genbank | 10-Mar-2020 | China | Fuyang | |
| MT292582 | Genbank | 06-Mar-2020 | Spain | Valencia | |
| MT292581 | Genbank | 27-Feb-2020 | Spain | Valencia | |
| MT292580 | Genbank | 27-Feb-2020 | Spain | Valencia | |
| MT292579 | Genbank | 09-Mar-2020 | Spain | Valencia | |
| MT292578 | Genbank | 09-Mar-2020 | Spain | Valencia | |
| MT292577 | Genbank | 08-Mar-2020 | Spain | Valencia | |
| MT292576 | Genbank | 10-Mar-2020 | Spain | Valencia | |
| MT292575 | Genbank | 10-Mar-2020 | Spain | Valencia | |
| MT292574 | Genbank | 02-Mar-2020 | Spain | Valencia | |
| MT292573 | Genbank | 09-Mar-2020 | Spain | Valencia | |
| MT292572 | Genbank | 10-Mar-2020 | Spain | Valencia | |
| MT292571 | Genbank | 09-Mar-2020 | Spain | Valencia | |
| MT292570 | Genbank | 10-Mar-2020 | Spain | Valencia | |
| MT292569 | Genbank | 09-Mar-2020 | Spain | Valencia | |
| MT276331 | Genbank | 29-Feb-2020 | USA | Texas | |
| MT276330 | Genbank | 28-Feb-2020 | USA | Florida | |
| MT276329 | Genbank | 28-Feb-2020 | USA | Florida | |
| MT276328 | Genbank | 27-Feb-2020 | USA | Oregon | |
| MT276327 | Genbank | 29-Feb-2020 | USA | Georgia | |
| MT276326 | Genbank | 29-Feb-2020 | USA | Georgia | |
| MT276325 | Genbank | 27-Feb-2020 | USA | Washington | |
| MT276324 | Genbank | 26-Feb-2020 | USA | California | |
| MT276323 | Genbank | 28-Feb-2020 | USA | Rhode Island | |
| MT263074 | Genbank | 10-Mar-2020 | Peru | ||
| MT256918 | Genbank | 06-Mar-2020 | Spain | Valencia | |
| MT256917 | Genbank | 02-Mar-2020 | Spain | Valencia | |
| MT198652 | Genbank | 05-Mar-2020 | Spain | Valencia | |
| MT233523 | Genbank | 04-Mar-2020 | Spain | Valencia | |
| MT233522 | Genbank | 02-Mar-2020 | Spain | Valencia | |
| MT233521 | Genbank | 27-Feb-2020 | Spain | Valencia | |
| MT233520 | Genbank | 26-Feb-2020 | Spain | Valencia | |
| MT233519 | Genbank | 27-Feb-2020 | Spain | Valencia | |
| MT226610 | Genbank | 20-Jan-2020 | China | ||
| MT198653 | Genbank | 08-Mar-2020 | Spain | Valencia | |
| MT198651 | Genbank | 04-Mar-2020 | Spain | Valencia | |
| MT163721 | Genbank | 01-Mar-2020 | USA | Washington | |
| MT163720 | Genbank | 01-Mar-2020 | USA | Washington | |
| MT163719 | Genbank | 01-Mar-2020 | USA | Washington | |
| MT163718 | Genbank | 29-Feb-2020 | USA | Washington | |
| MT163717 | Genbank | 28-Feb-2020 | USA | Washington | |
| MT163716 | Genbank | 27-Feb-2020 | USA | Washington | |
| MT126808 | Genbank | 28-Feb-2020 | Brazil | Sao Paulo | Traveler from Switzerland and Italy (Milan) to Brazil |
| MT066156 | Genbank | 30-Jan-2020 | Italy | ||
| MT295465 | Genbank | 27-Mar-2020 | USA | ||
| MT295464 | Genbank | 10-Mar-2020 | USA | ||
| MT093571 | Genbank | 07-Feb-2020 | Sweden | ||
| MT246667 | Genbank | 19-Jan-2020 | USA | Washington | |
| MT233526 | Genbank | 19-Jan-2020 | USA | Washington | |
| MT020781 | Genbank | 29-Jan-2020 | Finland | Lapland | |
| MT320891 | Genbank | 09-Mar-2020 | Iran | ||
| MT320538 | Genbank | Mar-2020 | France | ||
| MT300186 | Genbank | 02-Apr-2020 | USA | North Carolina | |
| MT281530 | Genbank | 09-Mar-2020 | Iran | ||
| MT291836 | Genbank | 29-Jan-2020 | China | Beijing | |
| MT291835 | Genbank | 27-Jan-2020 | China | Beijing | |
| MT291834 | Genbank | 28-Jan-2020 | China | Beijing | |
| MT291833 | Genbank | 28-Jan-2020 | China | Beijing | |
| MT291832 | Genbank | 25-Jan-2020 | China | Beijing | |
| MT291831 | Genbank | 24-Jan-2020 | China | Beijing | |
| MT291830 | Genbank | 30-Dec-2019 | China | Wuhan | |
| MT291829 | Genbank | 30-Dec-2019 | China | Wuhan | |
| MT291828 | Genbank | 30-Dec-2019 | China | Wuhan | |
| MT291827 | Genbank | 30-Dec-2019 | China | Wuhan | |
| MT291826 | Genbank | 30-Dec-2019 | China | Wuhan | |
| MT293225 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293224 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293223 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293222 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293221 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293220 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293219 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293218 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293217 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293216 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293215 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293214 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293213 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293212 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293211 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293210 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293209 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293208 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293207 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293206 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293205 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293204 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293203 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293202 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293201 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293200 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293199 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293198 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293197 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293196 | Genbank | 19-Mar-2020 | USA | Washington | |
| MT293195 | Genbank | 28-Mar-2020 | USA | Washington | |
| MT293194 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293193 | Genbank | 27-Mar-2020 | USA | Washington | |
| MT293192 | Genbank | 28-Mar-2020 | USA | Washington | |
| MT293191 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293190 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293189 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293188 | Genbank | 28-Mar-2020 | USA | Washington | |
| MT293187 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293186 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293185 | Genbank | 28-Mar-2020 | USA | Washington | |
| MT293184 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293183 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293182 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293181 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293180 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293179 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293178 | Genbank | 26-Mar-2020 | USA | Washington | |
| MT293177 | Genbank | 16-Mar-2020 | USA | ||
| MT293176 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293175 | Genbank | 30-Mar-2020 | USA | Washington | |
| MT293174 | Genbank | 27-Mar-2020 | USA | Washington | |
| MT293173 | Genbank | 30-Mar-2020 | USA | Washington | |
| MT293172 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293171 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293170 | Genbank | 18-Mar-2020 | USA | Washington | |
| MT293169 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293168 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293167 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293166 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293165 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293164 | Genbank | 17-Mar-2020 | USA | Washington | |
| MT293163 | Genbank | 29-Mar-2020 | USA | Washington | |
| MT293162 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT293161 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT293160 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT293159 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT293158 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT293157 | Genbank | 29-Mar-2020 | USA | Washington | |
| MT293156 | Genbank | 30-Mar-2020 | USA | Washington | |
| MT276598 | Genbank | Mar-2020 | Israel | ||
| MT276597 | Genbank | Feb-2020 | Israel | ||
| MT263469 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263468 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263467 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263466 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263465 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263464 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263463 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263462 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263461 | Genbank | 22-Mar-2020 | USA | Washington | |
| MT263460 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263459 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263458 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263457 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263456 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263455 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263454 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263453 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263452 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263451 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263450 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263449 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263448 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263447 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT263446 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263445 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263444 | Genbank | 20-Mar-2020 | USA | Washington | |
| MT263443 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263442 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263441 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263440 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263439 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263438 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263437 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263436 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263435 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263434 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263433 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263432 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263431 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263430 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263429 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263428 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263427 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263426 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263425 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263424 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263423 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263422 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263421 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263420 | Genbank | 20-Mar-2020 | USA | Washington | |
| MT263419 | Genbank | 20-Mar-2020 | USA | Washington | |
| MT263418 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263417 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263416 | Genbank | 21-Mar-2020 | USA | Washington | |
| MT263415 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263414 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263413 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263412 | Genbank | 22-Mar-2020 | USA | Washington | |
| MT263411 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263410 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263409 | Genbank | 22-Mar-2020 | USA | Washington | |
| MT263408 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263407 | Genbank | 22-Mar-2020 | USA | Washington | |
| MT263406 | Genbank | 21-Mar-2020 | USA | Washington | |
| MT263405 | Genbank | 21-Mar-2020 | USA | Washington | |
| MT263404 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263403 | Genbank | 20-Mar-2020 | USA | Washington | |
| MT263402 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263401 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263400 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263399 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263398 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263397 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263396 | Genbank | 22-Mar-2020 | USA | Washington | |
| MT263395 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263394 | Genbank | 22-Mar-2020 | USA | Washington | |
| MT263393 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263392 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263391 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263390 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263389 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263388 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263387 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263386 | Genbank | 22-Mar-2020 | USA | Washington | |
| MT263385 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263384 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263383 | Genbank | 24-Mar-2020 | USA | Washington | |
| MT263382 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT263381 | Genbank | 23-Mar-2020 | USA | Washington | |
| MT262916 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262915 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262914 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262913 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262912 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262911 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262910 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262909 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262908 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262907 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262906 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262905 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262904 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262903 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262902 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262901 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262900 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262899 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262898 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262897 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262896 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT262993 | Genbank | 12-Mar-2020 | Pakistan | Khyber Pakhtunkhwa | |
| MT259287 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259286 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259285 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259284 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259283 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259282 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259281 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259280 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259279 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259278 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259277 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259276 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259275 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259274 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259273 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259272 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259271 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259270 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259269 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259268 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259267 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259266 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259265 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259264 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259263 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259262 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259261 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259260 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259259 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259258 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259257 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259256 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259255 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259254 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259253 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259252 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259251 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259250 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259249 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259248 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259247 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259246 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259245 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT259244 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259243 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT259242 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT259241 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259240 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259239 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259238 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259237 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259236 | Genbank | 16-Mar-2020 | USA | Washington | |
| MT259235 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT258383 | Genbank | 18-Mar-2020 | USA | California | |
| MT258382 | Genbank | 18-Mar-2020 | USA | California | |
| MT258381 | Genbank | 18-Mar-2020 | USA | California | |
| MT258380 | Genbank | 18-Mar-2020 | USA | California | |
| MT258379 | Genbank | 18-Mar-2020 | USA | California | |
| MT258378 | Genbank | 18-Mar-2020 | USA | California | |
| MT258377 | Genbank | 18-Mar-2020 | USA | California | |
| MT256924 | Genbank | 11-Mar-2020 | Colombia | Antioquia | |
| MT259231 | Genbank | 25-Jan-2020 | China | Wuhan | |
| MT259230 | Genbank | 25-Jan-2020 | China | Wuhan | |
| MT259229 | Genbank | 26-Jan-2020 | China | Wuhan | |
| MT259228 | Genbank | 26-Jan-2020 | China | Wuhan | |
| MT259227 | Genbank | 26-Jan-2020 | China | Wuhan | |
| MT259226 | Genbank | 10-Jan-2020 | China | Wuhan | |
| MT253710 | Genbank | 21-Jan-2020 | China | Hangzhou | |
| MT253709 | Genbank | 21-Jan-2020 | China | Hangzhou | |
| MT253708 | Genbank | 21-Jan-2020 | China | Hangzhou | |
| MT253707 | Genbank | 25-Jan-2020 | China | Hangzhou | |
| MT253706 | Genbank | 22-Jan-2020 | China | Hangzhou | |
| MT253705 | Genbank | 22-Jan-2020 | China | Hangzhou | |
| MT253704 | Genbank | 25-Jan-2020 | China | Hangzhou | |
| MT253703 | Genbank | 25-Jan-2020 | China | Hangzhou | |
| MT253702 | Genbank | 21-Jan-2020 | China | Hangzhou | |
| MT253701 | Genbank | 21-Jan-2020 | China | Hangzhou | |
| MT253700 | Genbank | 25-Jan-2020 | China | Hangzhou | |
| MT253699 | Genbank | 24-Jan-2020 | China | Hangzhou | |
| MT253698 | Genbank | 23-Jan-2020 | China | Hangzhou | |
| MT253697 | Genbank | 23-Jan-2020 | China | Hangzhou | |
| MT253696 | Genbank | 23-Jan-2020 | China | Hangzhou | |
| MT251980 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT251979 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT251978 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT251977 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT251976 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT251975 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT251974 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT251973 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT251972 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246490 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT246489 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246488 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246487 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT246486 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246485 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT246484 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT246483 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT246482 | Genbank | 15-Mar-2020 | USA | Washington | |
| MT246481 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246480 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246479 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246478 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246477 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246476 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246475 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246474 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246473 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246472 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT246471 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246470 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246469 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246468 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246467 | Genbank | 14-Mar-2020 | USA | Washington | |
| MT246466 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246465 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246464 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246463 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246462 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246461 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246460 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT246459 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT246458 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT246457 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT246456 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246455 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT246454 | Genbank | 12-Mar-2020 | USA | Washington | |
| MT246453 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246452 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246451 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246450 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT246449 | Genbank | 13-Mar-2020 | USA | Washington | |
| MT240479 | Genbank | 04-Mar-2020 | Pakistan | Gilgit | |
| MT192773 | Genbank | 22-Jan-2020 | Viet Nam | Ho Chi Minh | |
| MT192772 | Genbank | 22-Jan-2020 | Viet Nam | Ho Chi Minh | |
| MT192765 | Genbank | 11-Mar-2020 | USA | California | |
| MT192759 | Genbank | 25-Jan-2020 | Taiwan | ||
| MT123293 | Genbank | 29-Jan-2020 | China | Guangzhou | |
| MT123292 | Genbank | 27-Jan-2020 | China | Guangzhou | |
| MT123291 | Genbank | 29-Jan-2020 | China | Guangzhou | |
| MT093631 | Genbank | 08-Jan-2020 | China | Wuhan | |
| MT121215 | Genbank | 02-Feb-2020 | China | Shanghai | |
| MT152824 | Genbank | 24-Feb-2020 | USA | Washington | |
| MT135044 | Genbank | 28-Jan-2020 | China | Beijing | |
| MT135043 | Genbank | 28-Jan-2020 | China | Beijing | |
| MT135042 | Genbank | 28-Jan-2020 | China | Beijing | |
| MT135041 | Genbank | 26-Jan-2020 | China | Beijing | |
| MT123290 | Genbank | 05-Feb-2020 | China | Guangzhou | |
| MT072688 | Genbank | 13-Jan-2020 | Nepal | Kathmandu | |
| MT066176 | Genbank | 05-Feb-2020 | Taiwan | Taipei | |
| MT066175 | Genbank | 31-Jan-2020 | Taiwan | Taipei | |
| MT050493 | Genbank | 31-Jan-2020 | India | Kerala | |
| MT049951 | Genbank | 17-Jan-2020 | China | Yunnan | |
| MT012098 | Genbank | 27-Jan-2020 | India | Kerala | |
| MN985325 | Genbank | 19-Jan-2020 | USA | Washington | Returned to Washington State from Wuhan (35 years old male) |
| MN996531 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKO00000000 |
| MN996530 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKN00000000 |
| MN996529 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKM00000000 |
| MN996528 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKL00000000 |
| MN996527 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKK00000000 |
| MN908947 | Genbank | 30-Dec-2019 | China | Wuhan | |
| MT188341 | Genbank | 05-Mar-2020 | USA | Minnesota | |
| MT188340 | Genbank | 07-Mar-2020 | USA | Minnesota | |
| MT188339 | Genbank | 09-Mar-2020 | USA | Minnesota | |
| MT184913 | Genbank | 24-Feb-2020 | USA | USA-CruiseA-26 | |
| MT184912 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-25 | |
| MT184911 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-24 | |
| MT184910 | Genbank | 18-Feb-2020 | USA | USA-CruiseA-23 | |
| MT184909 | Genbank | 21-Feb-2020 | USA | USA-CruiseA-22 | |
| MT184908 | Genbank | 21-Feb-2020 | USA | USA-CruiseA-21 | |
| MT184907 | Genbank | 18-Feb-2020 | USA | USA-CruiseA-19 | |
| LR757998 | Genbank | 26-Dec-2019 | China | Wuhan | synonym: CNA0007332 |
| LR757997 | Genbank | 31-Dec-2019 | China | Wuhan | synonym: CNA0007333 |
| LR757996 | Genbank | 01-Jan-2020 | China | Wuhan | synonym: CNA0007334 |
| LR757995 | Genbank | 05-Jan-2020 | China | Wuhan | synonym: CNA0007335 |
| MT159722 | Genbank | 21-Feb-2020 | USA | USA-CruiseA-6 | |
| MT159721 | Genbank | 21-Feb-2020 | USA | USA-CruiseA-5 | |
| MT159720 | Genbank | 21-Feb-2020 | USA | USA-CruiseA-4 | |
| MT159719 | Genbank | 18-Feb-2020 | USA | USA-CruiseA-3 | |
| MT159718 | Genbank | 18-Feb-2020 | USA | USA-CruiseA-2 | |
| MT159717 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-1 | |
| MT159716 | Genbank | 24-Feb-2020 | USA | USA-CruiseA-18 | |
| MT159715 | Genbank | 24-Feb-2020 | USA | USA-CruiseA-17 | |
| MT159714 | Genbank | 18-Feb-2020 | USA | USA-CruiseA-16 | |
| MT159713 | Genbank | 18-Feb-2020 | USA | USA-CruiseA-15 | |
| MT159712 | Genbank | 25-Feb-2020 | USA | USA-CruiseA-14 | |
| MT159711 | Genbank | 20-Feb-2020 | USA | USA-CruiseA-13 | |
| MT159710 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-9 | |
| MT159709 | Genbank | 20-Feb-2020 | USA | USA-CruiseA-12 | |
| MT159708 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-11 | |
| MT159707 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-10 | |
| MT159706 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-8 | |
| MT159705 | Genbank | 17-Feb-2020 | USA | USA-CruiseA-7 | |
| MT118835 | Genbank | 23-Feb-2020 | USA | California | |
| MT106054 | Genbank | 11-Feb-2020 | USA | Texas | |
| MT106053 | Genbank | 10-Feb-2020 | USA | California | |
| MT106052 | Genbank | 06-Feb-2020 | USA | California | |
| MT044258 | Genbank | 27-Jan-2020 | USA | California | |
| MT044257 | Genbank | 28-Jan-2020 | USA | Illinois | |
| MT039888 | Genbank | 29-Jan-2020 | USA | Massachusetts | |
| MT039887 | Genbank | 31-Jan-2020 | USA | Wisconsin | |
| MT039890 | Genbank | Jan-2020 | South Korea | ||
| MT039873 | Genbank | 20-Jan-2020 | China | Hangzhou | synonym: GWHABKS00000000 |
| MT027064 | Genbank | 29-Jan-2020 | USA | California | |
| MT027063 | Genbank | 29-Jan-2020 | USA | California | |
| MT027062 | Genbank | 29-Jan-2020 | USA | California | |
| MT020881 | Genbank | 25-Jan-2020 | USA | Washington | |
| MT020880 | Genbank | 25-Jan-2020 | USA | Washington | |
| MT019533 | Genbank | 01-Jan-2020 | China | Wuhan | synonym: GWHABKJ00000000 |
| MT019532 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKI00000000 |
| MT019531 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKH00000000 |
| MT019530 | Genbank | 30-Dec-2019 | China | Wuhan | synonym: GWHABKG00000000 |
| MT019529 | Genbank | 23-Dec-2019 | China | Wuhan | synonym: GWHABKF00000000 |
| MT007544 | Genbank | 25-Jan-2020 | Australia | Victoria | |
| MN997409 | Genbank | 22-Jan-2020 | USA | Arizona | |
| MN994468 | Genbank | 22-Jan-2020 | USA | California | |
| MN994467 | Genbank | 23-Jan-2020 | USA | California | |
| MN988713 | Genbank | 21-Jan-2020 | USA | Illinois | |
| MN988669 | Genbank | 02-Jan-2020 | China | Wuhan | |
| MN988668 | Genbank | 02-Jan-2020 | China | Wuhan | |
| MN975262 | Genbank | 11-Jan-2020 | China | Shenzhen | Traveler from Shenzhen to Wuhan (10 years old male) |
| MN938384 | Genbank | 10-Jan-2020 | China | Shenzhen | Traveler from Shenzhen to Wuhan (66 years old male) |
| LC521925 | Genbank | 25-Jan-2020 | Japan | Aichi | |
| LC522975 | Genbank | 31-Jan-2020 | Japan | Tokyo | |
| LC522974 | Genbank | 31-Jan-2020 | Japan | Tokyo | |
| LC522973 | Genbank | 29-Jan-2020 | Japan | Tokyo | |
| LC522972 | Genbank | 29-Jan-2020 | Japan | Kyoto | |
| MN996532 | Genbank | 24-Jul-2013 | China | Bat (Rhinolophus affinis) coronavirus RaTG13, synonym: GWHABKP00000000 | |
| MG772933 | Genbank | Feb-2017 | China | Bat (Rhinolophus sinicus) SARS-like coronavirus |
Meta data were supplemented from National Genomics Data Center (https://bigd.big.ac.cn/search).
1111111111111111111111111111222222222222222222222222222222222222222
111222333445555666678890011223444455566777777788899001134445555556666777777888888888889999 Sample Collection Date
468039046014240057368946742303120478837989233478807866263740363566891779233569001368888880135
913591646371306878191970873182110010726281427745863748698003293658174233728236794155678889802 - 2019 -||------------------------------------------- 2020 --------------------------------------------
043972162771622424039692272930136885740772763478406754826734549358094906674554794174381235837 30-Dec 10-Jan 20-Jan 30-Jan 10-Feb 20-Feb 29-Feb 10-Mar 20-Mar 30-Mar State/City
---------------------------------------------------------------------------------------------------------- -------|----------|---------|---------|----------|---------|--------|---------|---------|---------|---- ---------------------
MN908947.3 TGTCGCCTCCCCATGAGCCAGTAGCTCCGTGCTCGCCCGTCGTCCCCAACTCGGACCCACAACGTCCGGTGCCGTACCGCTCCCCGGGGCACG ● | | | | | | | | | 🇨🇳 Wuhan
MT019529.1 ............................................................................................. ● | | | | | | | | | | 🇨🇳 Wuhan
LR757998.1 ............................................................................................. ● | | | | | | | | | | 🇨🇳 Wuhan
MN996528.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MN996530.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MT019530.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MT019532.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MT291827.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MT291829.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MT291830.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MN996529.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
MN996531.1 ............................................................................................. ● | | | | | | | | | 🇨🇳 Wuhan
LR757996.1 ............................................................................................. | ● | | | | | | | | | 🇨🇳 Wuhan
MT019533.1 ............................................................................................. | ● | | | | | | | | | 🇨🇳 Wuhan
MN988668.1 ............................................................................................. | ● | | | | | | | | | 🇨🇳 Wuhan
MN988669.1 ............................................................................................. | ● | | | | | | | | | 🇨🇳 Wuhan
MT093631.2 ............................................................................................. | ● | | | | | | | | | 🇨🇳 Wuhan
MT039873.1 ............................................................................................. | | ● | | | | | | | 🇨🇳 Hangzhou
MT253701.1 ............................................................................................. | | |● | | | | | | | 🇨🇳 Hangzhou
MT253708.1 ............................................................................................. | | |● | | | | | | | 🇨🇳 Hangzhou
MT253709.1 ............................................................................................. | | |● | | | | | | | 🇨🇳 Hangzhou
MT253710.1 ............................................................................................. | | |● | | | | | | | 🇨🇳 Hangzhou
MT253702.1 ............................................................................................. | | |● | | | | | | | 🇨🇳 Hangzhou
MT253705.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT253696.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT253697.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT253698.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT253699.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT253700.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT192759.1 ............................................................................................. | | | ● | | | | | | | 🇹🇼
MT253703.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT253704.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT253707.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Hangzhou
MT291835.1 ............................................................................................. | | | ● | | | | | | | 🇨🇳 Beijing
MT044258.1 ............................................................................................. | | | ● | | | | | | | 🇺🇸 California
MT121215.1 ............................................................................................. | | | | ● | | | | | | 🇨🇳 Shanghai
MT066176.1 ............................................................................................. | | | | ● | | | | | | 🇹🇼 Taipei
MT118835.1 ............................................................................................. | | | | | | ● | | | | 🇺🇸 California
MT304482.1 ............................................................................................. | | | | | | |● | | | 🇺🇸 Illinois
MT188340.1 ............................................................................................. | | | | | | | ● | | | 🇺🇸 Minnesota
LC534419.1 ............................................................................................. | | | | | | | ●| | | 🇯🇵 Kanagawa
MT262993.1 ............................................................................................. | | | | | | | | ● | | 🇵🇰 Khyber Pakhtunkhwa
LC521925.1 .....T....................................................................................... | | | ● | | | | | | | 🇯🇵 Aichi
MT019531.1 .....................C....................................................................... ● | | | | | | | | | 🇨🇳 Wuhan
MT192772.1 ..........................T.................................................................. | | | ● | | | | | | | 🇻🇳 Ho Chi Minh
MT192773.1 ..........................T.................................................................. | | | ● | | | | | | | 🇻🇳 Ho Chi Minh
LC528232.1 ............................T................................................................ | | | | ● | | | | | 🇯🇵 Kanagawa
LC528233.1 ............................T................................................................ | | | | ● | | | | | 🇯🇵 Kanagawa
LC534418.1 ............................T................................................................ | | | | | ● | | | | | 🇯🇵 Kanagawa
MT276328.1 ............................T................................................................ | | | | | | ● | | | | 🇺🇸 Oregon
MT276597.1 ............................T................................................................ | | | | | | | | | | 🇮🇱
MT240479.1 ....A.......................T................................................................ | | | | | | | ● | | | 🇵🇰 Gilgit
MT320891.1 ....A.......................T................................................................ | | | | | | | ●| | | 🇮🇷
MT276324.1 ..................................T.......................................................... | | | | | | ● | | | | 🇺🇸 California
MT276325.1 ..................................T.......................................................... | | | | | | ● | | | | 🇺🇸 Washington
MT259230.1 ............................................T................................................ | | | ● | | | | | | | 🇨🇳 Wuhan
MT012098.1 ............................................T................................................ | | | ● | | | | | | | 🇮🇳 Kerala
MT039887.1 ............................................T................................................ | | | |● | | | | | | 🇺🇸 Wisconsin
MT259231.1 .......................................................T..................................... | | | ● | | | | | | | 🇨🇳 Wuhan
MT259228.1 .......................................................T..................................... | | | ● | | | | | | | 🇨🇳 Wuhan
MT259229.1 .......................................................T..................................... | | | ● | | | | | | | 🇨🇳 Wuhan
MT259227.1 .......................................................T..................................... | | | ● | | | | | | | 🇨🇳 Wuhan
MT020781.2 .........................................................T................................... | | | ●| | | | | | | 🇫🇮 Lapland
MT027064.1 .........................................................T................................... | | | ●| | | | | | | 🇺🇸 California
MT072688.1 ...........................................................T................................. | | ● | | | | | | | | 🇳🇵 Kathmandu
MT291828.1 ............................................................G................................ ● | | | | | | | | | 🇨🇳 Wuhan
MN996527.1 ............................................................G................................ ● | | | | | | | | | 🇨🇳 Wuhan
MT106053.1 ............................................................G................................ | | | | ● | | | | | 🇺🇸 California
MT039890.1 ....................................................................T........................ | | | | | | | | | | 🇰🇷
MN994468.1 ....................................................................T........................ | | | ● | | | | | | | 🇺🇸 California
MT007544.1 ....................................................................T........................ | | | ● | | | | | | | 🇦🇺 Victoria
MT093571.1 ....................................................................T........................ | | | | ● | | | | | | 🇸🇪
MT292572.1 ............................T.......................................T........................ | | | | | | | ● | | 🇪🇸 Valencia
MT281577.1 ............................T.......................................T........................ | | | | | | | ● | | 🇨🇳 Fuyang
MT304487.1 ............................T......T................................T........................ | | | | | | |● | | | 🇺🇸 Oregon
MT126808.1 ............................T......T......C.........................T........................ | | | | | | ●| | | | 🇧🇷 Sao Paulo
MT246454.1 ............................T......T......C.........................T........................ | | | | | | | | ● | | 🇺🇸 Washington
MT259267.1 ............................T......T......C.........................T........................ | | | | | | | | ● | | 🇺🇸 Washington
MT259285.1 ............G...............T......T............................C...T........................ | | | | | | | | ● | | 🇺🇸 Washington
MT263404.1 ............G...............T......T............................C...T........................ | | | | | | | | | ● | 🇺🇸 Washington
MT304474.1 ................T...........T......T................................T............T........... | | | | | | ● | | | | 🇰🇷
MT304475.1 ................T...........T......T................................T............T........... | | | | | | ● | | | 🇰🇷
MT304476.1 ................T...........T......T................................T............T........... | | | | | | ● | | | 🇰🇷
MT163716.1 .......C...T....T...........T......T................................T........................ | | | | | | ● | | | | 🇺🇸 Washington
MT276326.1 .......C...T....T...........T......T................................T........................ | | | | | | ● | | | 🇺🇸 Georgia
MT259226.1 ..........................................................................C.................. | ● | | | | | | | | 🇨🇳 Wuhan
MT263429.1 ...................................................................................T......... | | | | | | | | | ● | 🇺🇸 Washington
MT027062.1 .A.............G...................................................................T......... | | | ●| | | | | | | 🇺🇸 California
MT027063.1 .A.............G...................................................................T......... | | | ●| | | | | | | 🇺🇸 California
MT123290.1 .....................................T.....................................................T. | | | | ● | | | | | | 🇨🇳 Guangzhou
LC529905.1 .....................................T............................G........................T. | | | | | | | | | | 🇯🇵 Tokyo
LC522972.1 .....................................T............................G........................T. | | | ●| | | | | | | 🇯🇵 Kyoto
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MT192765.1 .........T.......................T........................G.................................. | | | | | | | |● | | 🇺🇸 California
MT263438.1 .........T.......................T........................G.................................. | | | | | | | | | ● | 🇺🇸 Washington
MT320538.1 .........T.......................T...T....................G.................................. | | | | | | | | | | 🇫🇷
MT276323.1 .........T.......................T....................G...G.................................. | | | | | | ●| | | | 🇺🇸 Rhode Island
MT304488.1 .........T.......................T....................G...G.................................. | | | | | | |● | | | 🇺🇸 Rhode Island
MT292569.1 .........T.......................T....................G...G.................................. | | | | | | | ●| | | 🇪🇸 Valencia
MT293219.1 .........T............G..........T....................G...G.................................. | | | | | | | | ● | | 🇺🇸 Washington
MT263433.1 .........T.......................T........................G....T............................. | | | | | | | | | ● | 🇺🇸 Washington
MT304490.1 .........T.......................T.................T......G....T............................. | | | | | | |● | | | 🇺🇸 Texas
MT251974.1 .........T.......................T.................T......G....T............................. | | | | | | | | ● | | 🇺🇸 Washington
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MT246451.1 .........T.......................T........................G...........................AAC.... | | | | | | | | ● | | 🇺🇸 Washington
MT259250.1 .........T.......................T........................G...........................AAC.... | | | | | | | | ● | | 🇺🇸 Washington
MT293209.1 .........T.......................T........................G...........................AAC.... | | | | | | | | ●| | 🇺🇸 Washington
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MT293210.1 ........................T.....................TG.T..............................C............ | | | | | | | | ●| | 🇺🇸 Washington
MT293202.1 ........................T.....................TG.T..............................C............ | | | | | | | | ●| | 🇺🇸 Washington
MT293216.1 ........................T.....................TG.T..............................C............ | | | | | | | | ●| | 🇺🇸 Washington
MT293206.1 ........................T.....................TG.T..............................C............ | | | | | | | | ●| | 🇺🇸 Washington
MT263444.1 ........................T.....................TG.T..............................C............ | | | | | | | | ● | 🇺🇸 Washington
MT263403.1 ........................T.....................TG.T..............................C............ | | | | | | | | ● | 🇺🇸 Washington
MT263405.1 ........................T.....................TG.T..............................C............ | | | | | | | | |● | 🇺🇸 Washington
MT263412.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263396.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263423.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263381.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263382.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263462.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263463.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263383.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263425.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263449.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263456.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263399.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263430.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263440.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263452.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263414.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT293185.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT293192.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT293188.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT293163.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ●| 🇺🇸 Washington
MT293157.1 ........................T.....................TG.T..............................C............ | | | | | | | | | ●| 🇺🇸 Washington
MT263434.1 .....T..................T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT259276.1 ......T.................T.....................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293177.1 ......T.................T.....................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸
MT152824.1 .................T......T.....................TG.T..............................C............ | | | | | | ● | | | | 🇺🇸 Washington
MT163720.1 .................T......T.....................TG.T..............................C............ | | | | | | |● | | | 🇺🇸 Washington
MT246455.1 .................T......T.....................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293184.1 .................T......T.....................TG.T....................A.........C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293211.1 .................T......T.....................TG.T....................A.........C............ | | | | | | | | ●| | 🇺🇸 Washington
MT246477.1 ..................T.....T.....................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT263424.1 ..................T.....T.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT246486.1 ..................T.....T.....................TG.T.......................T......C............ | | | | | | | | ● | | 🇺🇸 Washington
MT263398.1 ..................T.....T.....................TG.T.......................T......C............ | | | | | | | | | ● | 🇺🇸 Washington
MT293166.1 ...................G....T.....................TG.T............T.................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293218.1 ...................G....T.....................TG.T............T.................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT263458.1 ...................G....T...........T.........TG.T..............................C.........T.. | | | | | | | | | ● | 🇺🇸 Washington
MT263435.1 ...................G....T...........T.........TG.T..............................C.........T.. | | | | | | | | | ● | 🇺🇸 Washington
MT263419.1 .......................AT.....................TG.T..............................C............ | | | | | | | | ● | 🇺🇸 Washington
MT263464.1 .......................AT.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263400.1 .......................AT.....................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263416.1 ........................T...T.................TG.T..............................C............ | | | | | | | | |● | 🇺🇸 Washington
MT263395.1 ........................T...T.................TG.T..............................C............ | | | | | | | | | ● | 🇺🇸 Washington
MT246475.1 ........................T...T...........T.....TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246471.1 ........................T...T.................TG.T........................C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246457.1 ........................T......T..............TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT251980.1 ........................T......T..............TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246459.1 ........................T....................TTG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246476.1 ........................T....................TTG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT188341.1 ........................T.....................TG.T......T.......................C............ | | | | | | | ● | | | 🇺🇸 Minnesota
MT188339.1 ........................T.....................TG.T......T.......................C............ | | | | | | | ●| | | 🇺🇸 Minnesota
MT295464.1 ........................T.....................TG.T...........T..................C............ | | | | | | | ● | | 🇺🇸
MT259269.1 ........................T.....................TG.T...........T..................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293159.1 ........................T.....................TG.T...........T..................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246452.1 ........................T.....................TG.T.........................G....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246462.1 ........................T.....................TG.T.........................G....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293183.1 ........................T.....................TG.T.........................G....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT263457.1 ........................T.....................TG.T.........................G....C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263448.1 ........................T...............T.....TG.T.........................G....C............ | | | | | | | | | ● | 🇺🇸 Washington
MT246472.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262896.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262897.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262898.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262902.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262903.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262904.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262906.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262908.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT262909.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293225.1 ........................T....C................TG.T..............................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246478.1 ........................T.....................TG.T........................C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT251975.1 ........................T.....................TG.T........................C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT246489.1 ........................T.....................TG.T........................C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293179.1 ........................T.....................TG.T........................C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293190.1 ........................T.....................TG.T........................C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293194.1 ........................T.....................TG.T........................C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT263469.1 ........................T.....................TG.T........................C.....C............ | | | | | | | | | ● | 🇺🇸 Washington
MT246464.1 ........................T.....................TG.T......................T.C.....C............ | | | | | | | | ● | | 🇺🇸 Washington
MT263450.1 ........................T.....................TG.T......................T.C.....C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263447.1 ........................T..............G......TG.T.....................T........C............ | | | | | | | | ● | | 🇺🇸 Washington
MT263388.1 ........................T..............G......TG.T.....................T........C............ | | | | | | | | | ● | 🇺🇸 Washington
MT263422.1 ........................T..............G......TG.T.....................T........C............ | | | | | | | | | ● | 🇺🇸 Washington
MT259287.1 ........................T..................T..TGGT..T...........................C............ | | | | | | | | ● | | 🇺🇸 Washington
MT293169.1 ........................T..................T..TGGT..T...........................C............ | | | | | | | | ● | | 🇺🇸 Washington
MN938384.1 ........................T.......................................................C........T... | ● | | | | | | | | 🇨🇳 Shenzhen
MN975262.1 ........................T.......................................................C........T... | |● | | | | | | | | 🇨🇳 Shenzhen
MT291831.1 ........................T.......................................................C........T... | | | ● | | | | | | | 🇨🇳 Beijing
MT106054.1 ........................T.......................................................C........T... | | | | |● | | | | | 🇺🇸 Texas
MN997409.1 ........................T...T...................................................C........T... | | | ● | | | | | | | 🇺🇸 Arizona
LC522973.1 ........T...............T.......................................................C........T... | | | ●| | | | | | | 🇯🇵 Tokyo
LC522974.1 ........T...............T.......................................................C........T... | | | |● | | | | | | 🇯🇵 Tokyo
LC522975.1 ........T...............T.......................................................C........T... | | | |● | | | | | | 🇯🇵 Tokyo
MN996532.1 .........T............C.T..............C....T....T.........T...A.......T........C........T... | | | | | | | | | | 🦇
MG772933.1 .....A....A..C....T...C.T.........ATTT.GT.............C..G.T...A.G..............C.A......T... | | | | | | | | | | 🦇
| No. | Data type | Directory | Partition | Final LogLikelihood | AIC score | AICc score | BIC socre | # Free parameters |
|---|---|---|---|---|---|---|---|---|
| 1 | DNA | univ/uni/ | No partition | -62657.326781 | 126830.653562 | 126871.180612 | 133107.078890 | 758 |
| 2 | DNA | univ/3rd/ | Separate 3rd codon position and others | -62080.032512 | 125676.065024 | 125716.592074 | 131952.490352 | 758 |
| 3 | DNA | univ/sep/ | Separate each codon position | -61674.930991 | 124881.861982 | 124923.260094 | 131224.529266 | 766 |
| 4 | DNA | part/uni/ | Separate each ORF | -63290.960535 | 128199.921070 | 128246.164321 | 134898.638867 | 809 |
| 5 | DNA | part/3rd/ | Separate each ORF, 3rd codon position and others | -59946.218274 | 121618.436548 | 121671.155606 | 128764.287548 | 863 |
| 6 | DNA | part/sep/ | Separate each ORF, each codon position | -59816.294995 | 121420.589990 | 121477.224333 | 128823.128570 | 894 |
| Release Date | Contents |
|---|---|
| 28-Feb-2020 | initial release |
| 12-Mar-2020 | update genome sequence data, improve parallelization efficiency and usability of the scripts |
| 18-Mar-2020 | update genome sequence data |
| 20-Mar-2020 | update genome sequence data, remove USA-CruiseA data from the analyses |
| 23-Mar-2020 | update genome sequence data |
| 31-Mar-2020 | update genome sequence data |
| 05-Apr-2020 | update genome sequence data |
| 15-Apr-2020 | update genome sequence data, change MSA software, disable AA-based phylogenetic analyses |
| 01-May-2020 | update genome sequence data |
All in-house scripts in script/ direcory are released under the MIT license.
See also script/LICENSE.