New answers tagged phylogenetics
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 ...
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 ...
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 ...
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 ...
Math on Pandas Columns
The vectorised solution (fast) is, ...
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 ...
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