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1 vote

How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?

In the efetch.fcgi URL, you can set rettype=fasta to download the nucleotide sequence or ...
  • 111
1 vote
Accepted

Using R `ggtree`, attach extra data next to the nodes on an illustrated tree/newick file

I ended up using the following code to solve this issue: Change the tsv file and the tree file name accordingly. Be mindful of ...
  • 107
4 votes
Accepted

Plot phylogenetic tree from list of edges

The following example uses python to generate the newick string. You can than import that in R for further analysis. Please keep in mind that you can not use self reference for node4 (9,9,9), so I ...
  • 148
1 vote
Accepted

Is there a graphical/interactive 16S rRNA clustering method?

My recommendation is MegaX. It's the closest thing in phylogenetics to an all encompassing GUI. This has a nice visual alignment editor which highlights conserved, variable and parsimonious sites. It ...
  • 9,665
3 votes

Math on Pandas Columns

The vectorised solution (fast) is, ...
  • 9,665
1 vote

Phylogeny building in R from FASTA files:

The formal question I've been given is what aligner would I use? There is an issue between forming a data pipeline for ape and the latest and greatest. Its trade ...
  • 9,665

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