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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.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 ensemblesphagedisplay
Analysis tools for phage display experiments in the Harms Lablatticeproteins
2d protein lattice model simulator in PythonLove Open Source and this site? Check out how you can help us