harmslab/topiary

Stars
27
Rank 905,827 (Top 18 %)
Language
Python
License
MIT License
Created about 3 years ago
Updated over 1 year ago

harmslab/topiary

harmslab

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Python framework for doing ancestral sequence reconstruction

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

pytc

python program for analyzing isothermal titration calorimetry data

gpmap

A Python API for managing genotype-phenotype map data

hops

Use machine learning to find rules for peptide binding

Jupyter Notebook

fast_dbscan

fast, lightweight dbscan implementation for peptide strings

phylogenetics

A Python API for managing phylogenetics projects

notebooks-nonlinear-high-order-epistasis

Jupyter notebooks for Genetics paper, "Detecting high-order epistasis in nonlinear genotype-phenotype maps"

Jupyter Notebook

gpseer

A tool to predict missing data in sparsely sampled genotype-phenotype maps

pytc-demos

Set of jupyter notebooks illustrating the pytc API.

Jupyter Notebook

examl-tree-ancestor

pipeline stitching together fasttree, examl, and lazarus/paml for phylogenetics and ancestral sequence reconstruction

gpvolve

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 package

Jupyter Notebook

TreeViewer

Interactive Evolutionary Tree Viewer using D3.js

pytc-gui

PyQt5 GUI for pytc API

latticegpm

Python package for building fitness landscapes from protein lattice models

genotype-phenotype-maps

A curated list of experimental genotype-phenotype maps from published literature in JSON format

asr-protocol

Protocol and scripts for doing ancestral sequence reconstruction

Jupyter Notebook

flowsym

A Python API for simulating flow cytometry data.

gpgraph

NetworkX for genotype-phenotype maps

notebooks-epistasis-ensembles

Notebooks demonstrating the origins of high-order epistasis from statistical mechanical ensembles

Jupyter Notebook

phagedisplay

Analysis tools for phage display experiments in the Harms Lab

latticeproteins

2d protein lattice model simulator in Python