@neherlab

neherlab

Computational biology at the Biozentrum, Basel

  • Processing pipeline for pan-genome visulization and exploration

    Python 19 10 GPL-3.0 Updated Aug 17, 2018
  • Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

    Python 44 11 MIT Updated Aug 10, 2018
  • JavaScript 14 9 GPL-3.0 Updated Aug 6, 2018
  • A collection of documented examples using TreeTime

    Python Updated Aug 5, 2018
  • Control software for a morbidostat reactor based on arduino and python

    Python 2 1 Updated Jul 28, 2018
  • Analysis of fitness landscape of HIV-1 from longitudinal data

    Python 2 3 Updated Jul 1, 2018
  • Code for SIR models with antigenic evolution

    Matlab GPL-3.0 Updated Jun 17, 2018
  • JavaScript 1 1 Updated Mar 6, 2018
  • interactive flu trees side-by-side

    JavaScript MIT Updated Jan 31, 2018
  • Python MIT Updated Oct 31, 2017
  • Estimating time of HIV-1 infection from next-generation sequence diversity (code and data)

    Python 1 MIT Updated Sep 27, 2017
  • FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter i…

    C++ 7 7 GPL-3.0 Updated Apr 26, 2017
  • Establishment and stability of the latent HIV-1 DNA reservoir

    TeX 1 MIT Updated Feb 11, 2017
  • CSS 1 MIT Updated Nov 2, 2016
  • Python 2 2 MIT Updated Oct 28, 2016
  • Web application for deep sequencing on longitudinal HIV-1 samples from patients.

    JavaScript 3 Updated Oct 3, 2016
  • TeX Updated Jul 21, 2016
  • tool to build and visualize annotated influenza phylogenies based on blab/nextflu

    CSS 1 1 MIT Updated Jun 21, 2016
  • Generate and analyze beta coalescent trees

    Python 3 MIT Updated May 17, 2016
  • pipeline components for realtime virus analysis

    Python 1 1 MIT Updated May 6, 2016
  • Python wrapper of some SeqAn functions

    C++ 4 Updated Jan 16, 2016
  • Data processing pipeline for HIV next-gen sequencing

    Python 2 4 Updated Dec 8, 2015
  • Python 2 1 Updated Dec 7, 2015
  • Manuscript: Challenges with Using Primer IDs to Improve Accuracy of Next Generation Sequencing

    Python Updated Aug 3, 2015
  • Manuscript: Coalescence and genetic diversity in sexual populations under selection

    TeX Updated Aug 3, 2015
  • Manuscript: Inferring HIV Escape Rates from Multi-Locus Genotype Data

    TeX Updated Aug 3, 2015
  • Manuscript: Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution.

    TeX 2 1 Updated Jul 30, 2015
  • Prediction fitness of leaves on a genealogical tree

    Python 1 2 MIT Updated May 7, 2015
  • ImageJ plugins for blind decomposition of fluorencence microscopy data

    Java 4 1 MIT Updated Mar 24, 2015
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