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@harmslab Harms Lab @ University of Oregon

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    68 repositories

    • tfscreen

      Public
      Simulate or analyze a high-throughput screen of a transcription factor library
      Jupyter Notebook
      •
      MIT License
      •4•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • coraxlib

      Public
      C
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • raxml-ng

      Public
      RAxML Next Generation: faster, easier-to-use and more flexible
      C
      •
      GNU Affero General Public License v3.0
      •68•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • topiary-examples

      Public
      Jupyter notebooks demonstrating the topiary ancestral sequence reconstruction package
      Jupyter Notebook
      •
      MIT License
      •3•2•0•0•Updated Mar 25, 2026Mar 25, 2026

    • GeneRax

      Public
      C++
      •
      GNU Affero General Public License v3.0
      •12•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • topiary

      Public
      Python framework for doing ancestral sequence reconstruction
      pythonbioinformaticsphylogenetics
      pythonbioinformaticsphylogeneticsancestral-sequence-reconstructionevolutionary-biochemistry
      Python
      •
      MIT License
      •7•43•7•0•Updated Mar 20, 2026Mar 20, 2026

    • pll-modules

      Public
      High Level modules for the Low Level Phylogenetic Likelihood Library
      C
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • libpll-2

      Public
      Phylogenetic Likelihood Library 2 - experimental
      C
      •
      GNU Affero General Public License v3.0
      •14•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • GeneRaxCore

      Public
      Code used in both GeneRax and AleRax
      C++
      •3•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • terraphast-one

      Public
      An implementation of the SUPERB algorithm for analysis of phylogenetic terraces
      C++
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • MPIScheduler

      Public
      C++
      •2•0•0•0•Updated Mar 8, 2026Mar 8, 2026

    • eee

      Public
      ensemble epistasis engine
      Python
      •
      MIT License
      •2•0•0•0•Updated Aug 28, 2025Aug 28, 2025

    • dataprob

      Public
      Library for fitting models using a likelihood framework.
      Python
      •
      MIT License
      •2•4•0•1•Updated Sep 18, 2024Sep 18, 2024

    • linkage

      Public
      package for fitting thermodynamic linkage models to experimental data
      Jupyter Notebook
      •
      MIT License
      •2•0•0•1•Updated Sep 17, 2024Sep 17, 2024

    • ellipticbn

      Public
      tool for measuring ellipticity of cucurbituril macrocycles
      HTML
      •
      MIT License
      •1•2•0•0•Updated Jul 16, 2024Jul 16, 2024

    • setup_md

      Public
      Files and scripts used to set up MD simulations in the Harms Lab
      Python
      •
      MIT License
      •1•0•0•0•Updated May 14, 2024May 14, 2024

    • gpseer

      Public
      A tool to predict missing data in sparsely sampled genotype-phenotype maps
      pythonstatisticsevolution
      pythonstatisticsevolutionpredictionepistasisgenotype-phenotype-map
      Python
      •3•6•1•0•Updated Aug 18, 2023Aug 18, 2023

    • gpmap

      Public
      A Python API for managing genotype-phenotype map data
      geneticsevolutionnetworkx
      geneticsevolutionnetworkxgenotype-phenotype-maps
      Python
      •8•12•1•3•Updated Aug 18, 2023Aug 18, 2023

    • epistasis

      Public
      A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
      pythongeneticsevolution
      pythongeneticsevolutionmodelingnonlineargenotype-phenotype-mapsepistasishigh-order
      Python
      •
      The Unlicense
      •11•38•7•0•Updated Aug 18, 2023Aug 18, 2023

    • website

      Public
      Website for the lab
      HTML
      •
      MIT License
      •3•0•0•0•Updated Jan 16, 2023Jan 16, 2023

    • flowsym

      Public
      A Python API for simulating flow cytometry data.
      Python
      •
      MIT License
      •2•3•0•2•Updated Dec 26, 2022Dec 26, 2022

    • gpvolve

      Public
      A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.
      Python
      •
      MIT License
      •6•4•6•2•Updated Dec 26, 2022Dec 26, 2022

    • experimental-ensemble-epistasis

      Public
      Scripts and data for reproducing the analysis in "An experimental demonstration of ensemble epistasis in the lac repressor"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • riboswitch-epistasis

      Public
      calculations and analysis files for riboswitch ensemble epistasis manuscript
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 27, 2022Oct 27, 2022

    • asr-protocol

      Public
      Protocol and scripts for doing ancestral sequence reconstruction
      Jupyter Notebook
      •
      MIT License
      •3•2•1•1•Updated Oct 3, 2022Oct 3, 2022

    • stability-constraint-ms-figures

      Public
      code to generate figures and do analyses for hS100A9/M63F stability constraint study
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.9k•0•0•0•Updated Aug 7, 2022Aug 7, 2022

    • gpgraph

      Public
      NetworkX for genotype-phenotype maps
      Python
      •
      The Unlicense
      •4•1•0•1•Updated Aug 26, 2021Aug 26, 2021

    • gmx-template

      Public
      template for setting up MD simulations in the Harms lab.
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 16, 2021Apr 16, 2021

    • ensemble_epistasis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 7, 2021Apr 7, 2021
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