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Biopython Alternatives
Similar projects and alternatives to Biopython
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InfluxDB
InfluxDB – Built for High-Performance Time Series Workloads. InfluxDB 3 OSS is now GA. Transform, enrich, and act on time series data directly in the database. Automate critical tasks and eliminate the need to move data externally. Download now.
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Nim
Nim is a statically typed compiled systems programming language. It combines successful concepts from mature languages like Python, Ada and Modula. Its design focuses on efficiency, expressiveness, and elegance (in that order of priority).
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SaaSHub
SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives
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Pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
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tiny_python_projects
Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.
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adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
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SaaSHub
SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better Biopython alternative or higher similarity.
Biopython discussion
Biopython reviews and mentions
Posts with mentions or reviews of Biopython.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2024-10-17.
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How to Start Contributing to Open Source Software
I also like contributing specifically to my field. As a PhD student and possibly future scientist, I have a vested interest in the quality of the software in my field–specifically, structural bioinformatics. I use several tools in this field and often find areas that can be improved, both for myself and others. As an example, consider this minor documentation change I added to the Biopython documentation.
- Invitación a proyecto - Biopython en Español
- Biopython – Python Tools for Computational Molecular Biology
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comparing the similarity between a set of protein sequences
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.
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u/Responsible-Gas3852 comments on "Why is Cancer so Hard to Cure?"
Yes, the computing tool for biological computation.
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My boss is considering letting me take a programming course if I have some good reasons why.
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.
- Can you run ScanProsite locally?
- How to iterate over the whole GRCh38 genome with python?
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Help they’re turning me into a programmer
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...
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Biology related exercices and "challenges" to train by myself
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.
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A note from our sponsor - InfluxDB
www.influxdata.com | 18 Jun 2025
Stats
Basic Biopython repo stats
32
4,624
9.4
9 days ago
biopython/biopython is an open source project licensed under Freely Distributable which is not an OSI approved license.
The primary programming language of Biopython is Python.
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InfluxDB 3 OSS is now GA. Transform, enrich, and act on time series data directly in the database. Automate critical tasks and eliminate the need to move data externally. Download now.
www.influxdata.com