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    19 repositories

    • Cibiv.github.io

      Public
      CIBIV website
      HTML
      •0•2•0•0•Updated Oct 2, 2024Oct 2, 2024

    • GuaCAMOLE

      Public
      GuaCAMOLE (Guanosine Cytosine Aware Metagenomic Opulence Least squares Estimation) algorithm for the efficient detection and removal of GC bias from metagenomic samples
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Sep 26, 2024Sep 26, 2024

    • pyrganoid

      Public
      Python
      •0•1•0•0•Updated Apr 30, 2024Apr 30, 2024

    • EvoNAPS

      Public
      EvoNAPS is a database providing input parameter settings for extensive sequence simulations to be used in phylogenetic studies.
      Python
      •3•1•0•0•Updated Mar 13, 2024Mar 13, 2024

    • 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
      •4•1•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-selectionphylogenomicsultrafast-bootstrapmixture-modelmaximum-likelihoodiq-tree
      C++
      •
      GNU General Public License v2.0
      •44•184•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
      •190•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•43•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 them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids bias…
      c-plus-plus-11openclnext-generation-sequencingshort-read-mapper
      C++
      •
      Other
      •8•86•24•1•Updated May 15, 2019May 15, 2019

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.2k•0•0•0•Updated Feb 28, 2019Feb 28, 2019

    • PDA

      Public
      Phylogenetic Diversity Analyzer
      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)
      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