task-sequence-analysis

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Scindices / nanoporetech--dorado

Oxford Nanopore's Basecaller

status-active lang-python lang-cpp domain-bioinformatics interface-cli method-deep-learning role-application status-published status-packaged-conda scope-focused entity-nucleic-acid task-sequence-analysis entity-sequence interface-gpu domain-genomics

Updated Jul 22, 2026
C++

Scindices / iqtree--iqtree2

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IQ-TREE software version 2: phylogenetics by maximum likelihood

status-active lang-cpp domain-bioinformatics interface-cli role-application entity-protein status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence

Updated Jul 22, 2026
C++

Scindices / arq5x--bedtools2

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bedtools - the swiss army knife for genome arithmetic

status-active lang-cpp lang-c domain-bioinformatics interface-cli role-application task-file-io status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jun 10, 2026
C

Scindices / scverse--scanpy

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Single-cell analysis in Python. Scales to >100M cells.

status-active lang-python task-visualization domain-bioinformatics task-file-io interface-api status-published status-packaged-pypi status-packaged-conda method-machine-learning method-statistics role-toolkit scope-swissknife task-sequence-analysis entity-sequence domain-single-cell entity-multi-omics ecosystem-scverse

Updated Jul 28, 2026
Python

Scindices / microsoft--BioGPT

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lang-python status-archived domain-bioinformatics interface-cli method-deep-learning role-application interface-api status-published scope-focused domain-drug-discovery method-language-model task-sequence-analysis entity-sequence

Updated Jul 25, 2024
Python

Scindices / instadeepai--nucleotide-transformer

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Foundation Models for Genomics & Transcriptomics

status-active lang-python domain-bioinformatics method-deep-learning role-framework interface-api interface-jupyter status-published scope-focused entity-nucleic-acid method-language-model task-sequence-analysis entity-sequence domain-genomics

Updated Feb 24, 2026
Jupyter Notebook

Scindices / Biohub--esm

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status-active lang-python domain-bioinformatics interface-cli method-deep-learning role-framework domain-structural-biology entity-protein interface-api status-published scope-swissknife method-language-model task-sequence-analysis entity-sequence task-structure-prediction task-protein-design

Updated Jul 28, 2026
Jupyter Notebook

Scindices / seqan--seqan3

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The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

status-active task-alignment lang-cpp domain-bioinformatics task-file-io interface-api status-published method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jul 20, 2026
C++

Scindices / biotite-dev--biotite

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A comprehensive library for computational molecular biology

status-active lang-python domain-bioinformatics domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence

Updated Jul 21, 2026
Python

Scindices / biojava--biojava

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📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

status-active lang-java domain-bioinformatics domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence status-packaged-maven

Updated Jul 30, 2026
Java

Scindices / scikit-bio--scikit-bio

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scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

status-active lang-python task-alignment domain-bioinformatics task-file-io entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence

Updated Jul 28, 2026
Python

Scindices / DerrickWood--kraken2

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The second version of the Kraken taxonomic sequence classification system

status-active lang-python lang-cpp domain-bioinformatics interface-cli role-application status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jul 29, 2026
C++

Scindices / biopython--biopython

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Official git repository for Biopython (originally converted from CVS)

status-active lang-python domain-bioinformatics task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence ecosystem-biopython

Updated Jul 28, 2026
Python

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