Inspiration
The multi-step process from fasta to phylogenetic tree
What it does
Accepts a fasta file, generates an MSA file and a Newick tree with renamed leaves that can be used in your favorite phylogenetic tree visualizer.
How I built it
Python (deepnote for collaboration, visual studio for debugging)
Challenges I ran into
Using muscle through python.
Accomplishments that I'm proud of
Having an almost working program by the submission deadline. OS detecting auto-installer for muscle.
What I learned
It is difficult to make a unified automatic pipeline
What's next for FastNewPy
Actually working fully as intended. Adding checks for different fasta sequence ID formats and ability to name leaves based on these as well. Optionally automatically generating visualization of the phylogenetic tree.
Differences between presentation data and code: Clustal Omega used for MSA data in presentation.
Muscle used in code for MSA.
Jalview used for Newick tree file generation in presentation
Biopython used for Newick tree file generation in code.
iTOL used to create final presentation phylogenetic tree. https://itol.embl.de/
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