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    22 repositories

    • Cibiv.github.io

      Public
      CIBIV website
      HTML
      •0•2•0•0•Updated Apr 9, 2026Apr 9, 2026

    • GuaCAMOLE

      Public
      GuaCAMOLE (Guanosine Cytosine Aware Metagenomic Opulence Least squares Estimation) algorithm for the efficient detection and removal of GC bias from metagenomic…
      Python
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Mar 8, 2026Mar 8, 2026

    • EvoNAPS

      Public
      EvoNAPS is a database providing input parameter settings for extensive sequence simulations to be used in phylogenetic studies.
      Python
      •3•2•0•0•Updated Dec 11, 2025Dec 11, 2025

    • GenomicGCBiasCorrectionImprovesAbundanceEstimation

      Public
      Companion repository for the publication "Genomic GC bias correction improves species abundance estimation from metagenomic data"
      Python
      •
      Other
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • InSilicoSeq-GCBias

      Public
      :rocket: A sequencing simulator, forked to simulate GC bias
      Python
      •
      MIT License
      •36•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • quartetKAN

      Public
      Python
      •0•1•0•0•Updated Sep 29, 2025Sep 29, 2025

    • pyrganoid

      Public
      Python
      •0•1•0•0•Updated Feb 27, 2025Feb 27, 2025

    • SANjar

      Public
      Simulates the deterministic and stochastic versions of the SAN model
      R
      •0•0•0•0•Updated Feb 9, 2024Feb 9, 2024

    • ModelRevelator

      Public
      Python
      •
      MIT License
      •5•3•1•0•Updated Mar 28, 2023Mar 28, 2023

    • ipoolseq-pipeline

      Public
      A pipeline for the analysis of iPool-Seq data
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Feb 11, 2022Feb 11, 2022

    • IQ-TREE

      Public archive
      Efficient phylogenomic software by maximum likelihood
      phylogeneticsmodel-selectionmixture-model
      phylogeneticsmodel-selectionmixture-modelmaximum-likelihoodphylogenomicsiq-treeultrafast-bootstrap
      C++
      •
      GNU General Public License v2.0
      •45•209•94•2•Updated Nov 4, 2021Nov 4, 2021

    • trumicount

      Public
      Correctly counting molecules using unique molecular identifiers (UMIs)
      TeX
      •
      GNU Affero General Public License v3.0
      •1•9•2•0•Updated Sep 24, 2021Sep 24, 2021

    • gwpcR

      Public
      Corrects UMI-based NGS data for phantom UMIs and lost molecules using a mechanistic model of UMI-based experiments
      R
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Aug 23, 2021Aug 23, 2021

    • py-remoter

      Public
      Task queue which keeps tracks of jobs and their exit status
      0•0•0•0•Updated Aug 13, 2021Aug 13, 2021

    • zone-net

      Public
      Neural Network predicting if the underlying tree of a given MSA is a Farris- or Felsenstein-like tree
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated May 20, 2020May 20, 2020

    • UMI-tools

      Public
      Tools for handling Unique Molecular Identifiers in NGS data sets
      Python
      •
      MIT License
      •201•1•0•0•Updated Feb 29, 2020Feb 29, 2020

    • Teaser

      Public
      A tool to benchmark mappers and different parameters within minutes
      HTML
      •
      MIT License
      •10•44•4•0•Updated Jul 2, 2019Jul 2, 2019

    • NextGenMap

      Public
      NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming t…
      c-plus-plus-11openclnext-generation-sequencing
      c-plus-plus-11openclnext-generation-sequencingshort-read-mapper
      C++
      •
      Other
      •8•89•24•1•Updated May 15, 2019May 15, 2019

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.9k•0•0•0•Updated Feb 28, 2019Feb 28, 2019

    • PDA

      Public
      Phylogenetic Diversity Analyzer
      conservationphylogenetic-diversitybiodiversity
      conservationphylogenetic-diversitybiodiversity
      C++
      •
      GNU General Public License v2.0
      •3•0•1•0•Updated May 18, 2017May 18, 2017

    • cibiv-beamer-template

      Public
      CIBIV latex beamer template base on mtheme (https://github.com/matze/mtheme)
      templatelatexcibiv
      templatelatexcibivmtheme
      TeX
      •0•1•0•0•Updated Apr 28, 2017Apr 28, 2017

    • BODscore

      Public
      Scoring method for identified SNPs
      C
      •0•4•0•0•Updated Sep 9, 2015Sep 9, 2015
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