Explore projects
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Sam Nooij / R. gnavus comparative genomics
BSD 3-Clause "New" or "Revised" LicenseComparative genomics project of Ruminococcus gnavus, with additional prevalence and abundance analysis of worldwide metagenomic datasets.
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Mirrors / LOVD3
GNU General Public License v3.0 or laterMirror of https://github.com/LOVDnl/LOVD3.git
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Martin Larralde / PyJess
MIT LicenseCython bindings and Python interface to Jess, a 3D template matching software.
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Martin Larralde / Pyrodigal
GNU General Public License v3.0 onlyCython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
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Martin Larralde / gb-io.py
MIT LicenseA Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
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Martin Larralde / LightMotif
MIT LicenseA lightweight platform-accelerated library for biological motif scanning using position weight matrices.
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Sam Nooij / R. gnavus MAGs from rCDI patients
BSD 3-Clause "New" or "Revised" LicenseGenerate metagenome-assembled genomes of Ruminococcus gnavus from recurrent Clostridioides difficile infected patient metagenomes
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Martin Larralde / Scoring Matrices
MIT LicenseDependency free, Cython-compatible scoring matrices to use with biological sequences.
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Martin Larralde / Pyskani
MIT LicensePyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.
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Martin Larralde / PyOpal
MIT LicenseCython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
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Martin Larralde / OrthoANI
MIT LicenseA Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
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Martin Larralde / Torch TreeCRF
MIT LicenseA PyTorch implementation of Tree-structured Conditional Random Fields.
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Martin Larralde / PyFastANI
MIT LicenseCython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
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Martin Larralde / NAFcodec
MIT LicenseRust coder/decoder for Nucleotide Archival Format (NAF) files.
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Martin Larralde / Peptides.py
GNU General Public License v3.0 onlyPhysicochemical properties and indices for amino-acid sequences (ported from R).
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Martin Larralde / Mini 3Di
GNU General Public License v3.0 onlyA NumPy port of the foldseek code for encoding protein structures to 3di.
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Martin Larralde / PytrimAl
GNU General Public License v3.0 onlyCython bindings and Python interface to trimAl, a tool for automated alignment trimming.
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