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---

title: Phylogenetic trees

---

```bash

pip3 install ncbi-acc-download --user

pip3 install pyfasta

wget "https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(11118)&fq=%7B!tag=Flags_ss%7DFlags_ss:%22complete%22%20OR%20%22refseq%22&fq=HostLineageId_ss:(9606)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc&dlfmt=fasta&fl=id,Nucleotide_seq" -O genes/Coronaviridae/all.fasta

pyfasta split --header "genes/Coronaviridae/%(seqid)s.fasta" genes/Coronaviridae/all.fasta

```

```{r}

#install.packages("biomartr", dependencies = TRUE)

library(biomartr)

sequences <- read.csv(file = 'genes/Coronaviridae/sequences.csv')

head(sequences)

```

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