Explore projects
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Comparative genomics project of Ruminococcus gnavus, with additional prevalence and abundance analysis of worldwide metagenomic datasets.
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Cython bindings and Python interface to Jess, a 3D template matching software.
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Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
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A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
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A lightweight platform-accelerated library for biological motif scanning using position weight matrices.
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Generate metagenome-assembled genomes of Ruminococcus gnavus from recurrent Clostridioides difficile infected patient metagenomes
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Dependency free, Cython-compatible scoring matrices to use with biological sequences.
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PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.
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Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
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A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
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A PyTorch implementation of Tree-structured Conditional Random Fields.
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Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
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Physicochemical properties and indices for amino-acid sequences (ported from R).
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A NumPy port of the foldseek code for encoding protein structures to 3di.
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Cython bindings and Python interface to trimAl, a tool for automated alignment trimming.
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