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intro_python
Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.marginPhase
sonLib
Small general purpose library for C and Python with focus on bioinformatics.jobTree
Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)pinchesAndCacti
Library for constructing pinch graphs and cactus graphspecan
Probabilistic consistency based alignerortheus
Evolutionary transducer based method for aligning and reconstructing indel historiesassemblaScripts
Benchmarking scripts for assessing assemblies, used in the Assemblathon 1 projectassemblaLib
Library for Assemblathon 1 analysis scriptscactusTools
A home for various common but non-essential scripts for the cactus projectpysqg
Prototype implementation of SQG parser in PythonmatchingAndOrdering
Library of matching and ordering algorithms, used for "reference problem"Progressive-Alignment-with-Cactus
referenceScripts
Scripts for evaluating a cactus reference genomeprogressiveBenchmarks
Evaluation scripts for testing cactus progressive methodLove Open Source and this site? Check out how you can help us