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pdbtools
A set of tools for manipulating and doing calculations on wwPDB macromolecule structure filesepistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.topiary
Python framework for doing ancestral sequence reconstructionpytc
python program for analyzing isothermal titration calorimetry datagpmap
A Python API for managing genotype-phenotype map datahops
Use machine learning to find rules for peptide bindingfast_dbscan
fast, lightweight dbscan implementation for peptide stringsphylogenetics
A Python API for managing phylogenetics projectsnotebooks-nonlinear-high-order-epistasis
Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"gpseer
A tool to predict missing data in sparsely sampled genotype-phenotype mapspytc-demos
Set of jupyter notebooks illustrating the pytc API.examl-tree-ancestor
pipeline stitching together fasttree, examl, and lazarus/paml for phylogenetics and ancestral sequence reconstructiongpvolve
A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.dataprob
Library for fitting models using a likelihood framework.topiary-examples
Jupyter notebooks demonstrating the topiary ancestral sequence reconstruction packageTreeViewer
Interactive Evolutionary Tree Viewer using D3.jspytc-gui
PyQt5 GUI for pytc APIlatticegpm
Python package for building fitness landscapes from protein lattice modelsgenotype-phenotype-maps
A curated list of experimental genotype-phenotype maps from published literature in JSON formatasr-protocol
Protocol and scripts for doing ancestral sequence reconstructionflowsym
A Python API for simulating flow cytometry data.gpgraph
NetworkX for genotype-phenotype mapsnotebooks-epistasis-ensembles
Notebooks demonstrating the origins of high-order epistasis from statistical mechanical ensembleslatticeproteins
2d protein lattice model simulator in PythonLove Open Source and this site? Check out how you can help us