61 projects
pyjess
Cython bindings and Python interface to JESS, a 3D template matching software.
chamois-tool
Chemical Hierarchy Approximation for secondary Metabolism clusters Obtained In Silico.
gb-io
A Python interface to gb-io, a fast GenBank parser and serializer written in Rust.
pronto
Python frontend to ontologies.
pycomsa
Cython bindings and Python interface to CoMSA, a compressor for multiple-sequence alignments.
pyswrd
Cython bindings and Python interface to SWORD (Smith Waterman On Reduced Database), a heuristic method for fast database search.
pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated pairwise aligner.
pyrodigal
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.
pyfamsa
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
orthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement. (renamed to pyorthoani)
pyorthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
fastobo
Faultless AST for Open Biomedical Ontologies in Python.
nafcodec
PyO3 bindings and Python interface to nafcodec, an encoder/decoder for Nucleotide Archive Format (NAF) files.
pyfastani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
pyhmmer
Cython bindings and Python interface to HMMER3.
sphinxcontrib-svgbob
A Sphinx extension to convert ASCII diagrams to SVGs with Svgbob.
pyncbitk
Cython bindings and Python interface to the NCBI C++ Toolkit.
pyskani
PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.
igua
High-throughput method for gene cluster family identification.
pysylph
PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.
diced
Rust re-implementation of the MinCED algorithm to Detect Instances of CRISPRs in Environmental Data.
pytantan
Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.
scoring-matrices
Dependency free, Cython-compatible scoring matrices to use with biological sequences.
mini3di
A NumPy port of the foldseek code for encoding structures to 3di.
peptides
Physicochemical properties, indices and descriptors for amino-acid sequences.
lightmotif
PyO3 bindings and Python interface to lightmotif, a library for platform-accelerated biological motif scanning using position weight matrices.
pytrimal
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming.
pyrodigal-gv
A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.
rlinalg
Linear Algebra routines for Python as implemented in the R language.
pymemesuite
Cython bindings and Python interface to the MEME suite.
gecco-tool
Gene cluster prediction with Conditional random fields.
torch-treecrf
A PyTorch implementation of Tree-structured Conditional Random Fields.
nmrml2isa
nmrml2isa - nmrML to ISA-Tab parsing tool
fs.sshfs
Pyfilesystem2 over SSH using paramiko
btyper3
In silico taxonomic classification of Bacillus cereus group isolates using assembled genomes
fs.smbfs
Pyfilesystem2 over SMB using pysmb
iocursor
A zero-copy file-like wrapper for byte buffers, inspired by Rust's std::io::Cursor.
mzml2isa
mzML file parser and converter to ISA-Tab
rich-msa
A Rich renderable for viewing Multiple Sequence Alignments in the terminal.
fs
Python's filesystem abstraction layer
fs.archive
Enhanced archive filesystems for Pyfilesystem2
moclo
A Python implementation of the MoClo system logic.
ffpb
A progress bar for ffmpeg. Yay !
instalooter
Another API-less Instagram pictures and videos downloader
Gecco
Generic Environment for Context-Aware Correction of Orthography
nanoset
A memory-optimized wrapper for Python sets likely to be empty.
pyhcrf
A hidden (state) conditional random field (HCRF) implementation written in Python and Cython.
property-cached
A decorator for caching properties in classes (forked from cached-property).
jinja2-fsloader
A Jinja2 template loader using PyFilesystem2
moclo-ecoflex
EcoFlex implementation for the base moclo library.
moclo-ytk
Yeast ToolKit implementation for the base moclo library.
moclo-cidar
CIDAR implementation for the base moclo library.
bindings.rust
A namespace for Python bindings to Rust libraries
bindings.cpp
A namespace for Python bindings to C++ libraries
bindings.c
A namespace for Python bindings to C libraries
bindings
A namespace for Python binding modules
fs.proxy
Miscellaneous proxy filesystems for Pyfilesystem2
dockerasmus
An easy to use docking library.
imzml2isa-qt
A PyQt interface for mzml2isa parser.
mzml2isa-qt
A PyQt interface for mzml2isa parser.
nmrml2isa-qt
A PyQt interface for nmrml2isa parser.
