Top 6 Python Phylogenetic Projects
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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.
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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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ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
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GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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ielex-data-and-tree
Data and scripts for producing a Baysian phylogenetic tree sample of for the Indo-European family which is "good enough", using data from IELex (Dunn et al. 2011).
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Python Phylogenetics discussion
Python Phylogenetics related posts
Index
What are some of the best open-source Phylogenetic projects in Python? This list will help you:
| # | Project | Stars |
|---|---|---|
| 1 | Biopython | 4,588 |
| 2 | ete | 826 |
| 3 | GTDBTk | 521 |
| 4 | ClipKIT | 73 |
| 5 | ielex-data-and-tree | 7 |
| 6 | taxopedia | 7 |
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