Alternatives and similar repositories for ACE

Users that are interested in ACE are comparing it to the libraries listed below

• ihh / trajectory-likelihood
  Calculate indel trajectory likelihoods using methods of Miklós, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)
  ☆14Updated 3 years ago
• Emergent-Behaviors-in-Biology / community-simulator
  Simulate microbial community batch culture experiments.
  ☆42Updated 10 months ago
• phylovi / bito
  Python-interface C++ library for Bayesian phylogenetics via optimization
  ☆39Updated last year
• harmslab / epistasis
  A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
  ☆35Updated 2 years ago
• caseywdunn / phylogenetic_biology
  A book for my course
  ☆17Updated 10 months ago
• lanl / PyBNF
  An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuris…
  ☆24Updated last month
• christiaanjs / treeflow
  ☆13Updated 10 months ago
• GPZ-Bioinfo / tmap
  topological data analysis of population-scale microbiomes
  ☆31Updated 2 years ago
• SBRG / cobrame
  A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
  ☆35Updated 6 years ago
• usnistgov / lantern
  Interpretable genotype-phenotype landscape modeling
  ☆35Updated last year
• dmnfarrell / pybioviz
  bioinformatics visualization tools with pyviz/bokeh
  ☆20Updated last year
• sjspielman / pyvolve
  Python library to simulate evolutionary sequence data
  ☆80Updated 3 years ago
• RuleWorld / bionetgen
  Rule-based modeling framework
  ☆65Updated 3 months ago
• pstjohn / dFBA
  Dynamic Flux Balance analysis in Python
  ☆11Updated 9 years ago
• ElisabethRoesch / Perspective_Julia_for_Biologists
  Online material for the Perspective: "Julia for Biologists" presented at JuliaCon 2021: https://www.youtube.com/watch?v=gRj7E5kYG1I
  ☆100Updated 2 years ago
• ybrandvain / GRFP
  Here are a set of example Relevant Background and Future Goals and Graduate Research Plan Statement statements for the NSF GRFP in Ecolog…
  ☆72Updated 6 years ago
• broadinstitute / pyro-cov
  Pyro models of SARS-CoV-2 variants
  ☆77Updated last year
• PhysiBoSS / PhysiBoSS
  PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
  ☆26Updated this week
• gchure / reproducible_research
  A template repository for how I structure my scientific research
  ☆99Updated last year
• phiweger / nanotext
  Proteins as words, genomes as documents.
  ☆19Updated 4 years ago
• matthiaskoenig / dfba
  Encoding Dynamic Flux Balance Analysis in SBML
  ☆12Updated 5 years ago
• pablocarderam / opqua
  Epidemiological modeling framework for pathogen population genetics and evolution.
  ☆18Updated 11 months ago
• alubbock / microbench
  Benchmarking and metadata tracking for Python. Extensible, with distributed/cluster support.
  ☆19Updated last week
• WarrenWeckesser / heatmapcluster
  A python library for generating a clustered heatmap with dendrograms.
  ☆34Updated 3 years ago
• cdanielmachado / framed
  framed: a metabolic modeling package for python
  ☆26Updated 5 years ago
• phievo / phievo
  Software for in silico evolution - Paul François' group McGill University
  ☆10Updated 3 years ago
• matthiaskoenig / cy3sbml
  cy3sbml: SBML for Cytoscape 3
  ☆14Updated last week
• ialbert / booleannet
  Boolean Network Modeling
  ☆40Updated 5 years ago
• asntech / postdoc-funding-schemes
  Funding schemes and travel grant opportunities for postdocs
  ☆54Updated 6 years ago
• Edinburgh-Genome-Foundry / Primavera
  Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.
  ☆33Updated 5 months ago