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Applied Computational Genomics Team

Computational Genomics tools from Maria Anisimova and collaborators

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  1. tral tral Public

    Tandem Repeat Annotation Library

    Python 24 7

  2. ProGraphMSA ProGraphMSA Public

    ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in…

    C++ 9 4

  3. bpp-arpip bpp-arpip Public

    ARPIP: Ancestral sequence Reconstruction under PIP

    C++ 9 1

  4. ProPIP ProPIP Public

    C++ 5 3

  5. webSTR-API webSTR-API Public

    WebSTR-API: programmatic access to WebSTR, database of Human genome-wide variation in Short Tandem Repeats (STRs)

    Python 5 4

  6. rust-phylo rust-phylo Public

    Phylo library in Rust

    Rust 2 1

Repositories

Showing 10 of 37 repositories
  • STR-density Public

    Scripts and background to determine short tandem repeat (STR) densities in genes and genomes

    acg-team/STR-density’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Nov 15, 2024
  • rust-phylo Public

    Phylo library in Rust

    acg-team/rust-phylo’s past year of commit activity
    Rust 2 MIT 1 0 1 Updated Nov 13, 2024
  • ConSTRain Public

    A short tandem repeat variant caller that incorporates copy number information

    acg-team/ConSTRain’s past year of commit activity
    Rust 0 GPL-3.0 0 0 0 Updated Nov 11, 2024
  • acg-team/multicancer_STR’s past year of commit activity
    0 MIT 0 0 0 Updated Nov 7, 2024
  • acg-team/Indel-Pattern-Analysis-HIV’s past year of commit activity
    Python 0 0 0 0 Updated Oct 2, 2024
  • webSTR-API Public

    WebSTR-API: programmatic access to WebSTR, database of Human genome-wide variation in Short Tandem Repeats (STRs)

    acg-team/webSTR-API’s past year of commit activity
    Python 5 MIT 4 0 1 Updated Aug 6, 2024
  • single-char-indel-ASR-preserves-long-indels Public

    This repository includes the scripts used for analysis investigating the dynamics of indels in mammalian orthologous proteins and the examination of the ancestral reconstruction of multiple-character indels under the PIP.

    acg-team/single-char-indel-ASR-preserves-long-indels’s past year of commit activity
    Jupyter Notebook 0 GPL-3.0 0 0 1 Updated Jul 31, 2024
  • acg-team/Bioinfo4B’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Jun 7, 2024
  • Bioinfo4B-STR Public

    Short tandem repeat project for the course "Bioinformatics for Beginners"

    acg-team/Bioinfo4B-STR’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated May 27, 2024
  • acg-team/Selection-in-Genes-Course’s past year of commit activity
    0 GPL-3.0 1 0 0 Updated May 21, 2024

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