Biopython VS Dask

Usearch will do all-against-all comparisons, cluster sequences, and produce alignments for each cluster. You can set the clustering threshold (proportion of residues identical). The alignments are in fasta format, which is pretty standard. If all you want is basic similarity it might be easiest to just write something that calculates normalized Hamming distances (typically called p-distances in the molecular evolution literature) between pairs of sequences. I suspect the biopython fasta reader (you can install biopython from https://biopython.org/) will be good enough.

Yes, the computing tool for biological computation.

Beside that their core lectures to non-computer scientists are public (survey), workshops by software carpentry move around the globe. Maybe your intent to seed hands-on knowledge is in similar tune before heading for biopython, bioperl, bioawk. It doesn't hurt to tap into resources initially written for non-labrats either, e.g. about regular expressions by programming historian.

Well, what language do you want to learn? What is your background so far? Assuming it is more on the side of biology, software carpentry's Python may eventually lead to biopython? Though there equally is a chance for AWK (Hack the planet's text! and bioawk...

I think you mind find something of a community around BioPython, which might be helpful. Just looking at the capabilities will probably be instructive as well.

Python is the main programming language I use nowadays. In particular numpy and pandas are of course extremely useful. I also use biopython package - a collection of software tools for biological computation written in Python by an international group of researchers and developers.

Data scientists work on phenomenally large datasets, and Dask is a handy tool for exploration within the confines of a single cloud VM or their local PCs. Location data visualization is an essential part of deciding further algorithm development and roadmap for projects. This lays the foundation for data engineering and science to work at scale, with petabytes of data.

Dask

We're using a lot of Python. In addition to these, gridMET, Dask, HoloViz, and kerchunk.

I wrote this for speeding up the RPC messaging in dask, but figured it might be useful for others as well. The source is available on github here: https://github.com/jcrist/msgspec.

Dask: Distributed data frames, machine learning and more

To do that, we are efficiently using Dask, simply creating on-demand local (or remote) clusters on task run() method:

Look into Dask, see: https://dask.org/

[1] https://dask.org/