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    19 repositories

    • learnMSA

      Public
      Learning and Aligning Large Protein Families with support of protein language models.
      Jupyter Notebook
      •
      MIT License
      •4•20•4•0•Updated Feb 12, 2025Feb 12, 2025

    • Tiberius

      Public
      Tiberius is a deep learning gene finder.
      Python
      •
      MIT License
      •4•47•12•0•Updated Feb 8, 2025Feb 8, 2025

    • GALBA

      Public
      GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
      Perl
      •
      Other
      •4•139•10•1•Updated Jan 27, 2025Jan 27, 2025

    • BRAKER

      Public
      BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
      Perl
      •
      Other
      •84•377•164•1•Updated Jan 22, 2025Jan 22, 2025

    • Augustus

      Public
      Genome annotation with AUGUSTUS
      geneannotationgenomediscoveryprediction
      C++
      •112•293•158•6•Updated Jan 6, 2025Jan 6, 2025

    • webaugustus

      Public
      Groovy
      •0•0•0•0•Updated Dec 8, 2024Dec 8, 2024

    • clamsa

      Public
      ClaMSA (Classify Multiple Sequence Alignments).
      Python
      •2•11•4•0•Updated Nov 21, 2024Nov 21, 2024

    • TSEBRA

      Public
      TSEBRA: Transcript Selector for BRAKER
      Python
      •7•47•12•0•Updated Nov 13, 2024Nov 13, 2024

    • MakeHub

      Public
      Fully automated generation of UCSC assembly hubs
      Python
      •
      GNU General Public License v3.0
      •4•34•1•0•Updated Oct 2, 2024Oct 2, 2024

    • Diatom_annotation_scripts

      Public
      Helper scripts to prepare a functionally decorated BRAKER output file for upload to NCBI Genomes
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • tf_tcmc

      Public
      Tensorflow Implementation for calculating graphical probabilistical models with edge transitions modelled by Time-reversible Continuous-time Markov Chains (TCMC).
      Python
      •1•2•1•0•Updated Aug 16, 2024Aug 16, 2024

    • VARUS

      Public
      RNA-Seq sampling
      C++
      •
      Other
      •2•8•4•0•Updated Jul 1, 2024Jul 1, 2024

    • pygustus

      Public
      Python wrapper for AUGUSTUS.
      Python
      •
      Apache License 2.0
      •0•2•3•0•Updated Feb 28, 2023Feb 28, 2023

    • TSEBRA-experiments

      Public
      Documentation of the Experiments for the TSEBRA paper.
      Python
      •1•0•0•0•Updated Jul 6, 2021Jul 6, 2021

    • GeometricHashing

      Public
      Global, Highly Specific and Fast Filtering of Alignment Seeds
      C++
      •
      GNU General Public License v3.0
      •1•4•0•0•Updated Mar 9, 2021Mar 9, 2021

    • GUSHR

      Public
      Generating UTRs from SHort Reads
      Python
      •
      GNU General Public License v3.0
      •2•11•8•0•Updated Sep 28, 2020Sep 28, 2020

    • AugustusDeveloperTest

      Public
      Tests and Test Outputs for AUGUSTUS Development
      0•0•0•0•Updated Jan 14, 2020Jan 14, 2020

    • PeptImprove

      Public
      Pipeline for fully automated prokaryotic genome annotation with peptide data from MS/MS experiments
      Python
      •0•2•0•0•Updated Sep 19, 2019Sep 19, 2019

    • taxonomy

      Public
      Taxonomy database and related questions, e.g. closest taxon in a given set
      Python
      •1•2•0•0•Updated Jun 26, 2019Jun 26, 2019