New answers tagged phylogenetics
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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 ...
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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 ...
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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 ...
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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 ...
M__♦
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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 ...
M__♦
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