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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 alignercPecan
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.assemblaScripts
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