Rasusa — Peer-reviewed • Rank 17.1 • Science 93%

Rasusa: Randomly subsample sequencing reads to a specified coverage - Published in JOSS (2022)

mrivis — Peer-reviewed • Rank 9.8 • Science 93%

mrivis: Medical image visualization library for neuroscience in python - Published in JOSS (2018)

Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer — Peer-reviewed • Rank 8.9 • Science 93%

Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer - Published in JOSS (2019)

pandas • Rank 40.8 • Science 59%

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

Recan — Peer-reviewed • Rank 6.1 • Science 93%

Recan: Python tool for analysis of recombination events in viral genomes - Published in JOSS (2020)

scikit-fda • Rank 19.4 • Science 67%

Functional Data Analysis Python package

segul • Rank 15.8 • Science 67%

An ultrafast and memory efficient tool for phylogenomics

trajectopy • Rank 11.1 • Science 67%

Trajectopy - Trajectory Evaluation in Python

nanoseq • Rank 8.8 • Science 67%

Nanopore demultiplexing, QC and alignment pipeline

filtersam • Rank 6.3 • Science 67%

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

pxblat • Rank 9.5 • Science 59%

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

ska • Rank 15.4 • Science 44%

Split k-mer analysis – version 2

pypar • Rank 12.4 • Science 44%

Phoneme alignment representation compatible with multiple forced aligners

align-cli • Rank 11.9 • Science 44%

A CLI for pairwise alignment of sequences, using both normal and mass based alignment.

pyfoal • Rank 10.7 • Science 44%

Python forced alignment

rmsd • Rank 17.6 • Science 36%

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

callsync • Rank 6.4 • Science 39%

R package to align recordings, detect, assign, trace and analyse vocalisations

astred • Rank 3.2 • Science 41%

An easy-to-use library to linguistically compare one sentence and its words to another, in the same language or a different one. For instance useful for comparing a translation with the original text, to find differences and similarities between two different translations, or to see how a machine translation differs from a reference translation.

https://github.com/bertsky/nmalign • Rank 6.5 • Science 36%

forced alignment of lists of string by fuzzy string matching

visualqc • Rank 10.5 • Science 26%

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.

https://github.com/astrazeneca/onto_merger • Rank 8.0 • Science 23%

OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.

nrex • Rank 2.5 • Science 26%

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

https://github.com/astorfi/llm-alignment-project • Rank 3.5 • Science 23%

A comprehensive template for aligning large language models (LLMs) using Reinforcement Learning from Human Feedback (RLHF), transfer learning, and more. Build your own customizable LLM alignment solution with ease.

fluentdna • Rank 9.0 • Science 13%

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

BALCONY • Rank 3.5 • Science 13%

R package: BALCONY (Better ALignment CONsensus analYsis)

https://github.com/cancerit/pygas • Rank 1.4 • Science 10%

python Guide aligned Sequences

nf-fastq2bam • Science 57%

Nextflow pipeline to convert FASTQ files to BAM for WGS and RNA-seq data

microaligner • Science 44%

Image registration (alignment) software for large microscopy images

goombay • Science 67%

Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.

variantcalling • Science 65%

Nextflow DSL2 pipeline to call variants on long read alignment.

relationship-between-auditory-and-semantic-entrainment • Science 44%

Relationship between auditory and semantic entrainmnet

https://github.com/cyberagentailab/annotation-efficient-po • Science 23%

Code of "Annotation-Efficient Preference Optimization for Language Model Alignment"

https://github.com/cyberagentailab/filtered-dpo • Science 23%

Introducing Filtered Direct Preference Optimization (fDPO) that enhances language model alignment with human preferences by discarding lower-quality samples compared to those generated by the learning model

https://github.com/cnr-ibba/nf-chip-alignment • Science 23%

Align chip probes to a reference genome

pacvar • Science 57%

Longread PacBio sequencing processing for WGS and PureTarget

mapsea • Science 57%

Mapping And Prediction of Shared Elements in Alignments

https://github.com/bencardoen/smlmtools.jl • Science 36%

Computational tools for single molecule localization / superresolution microscopy (point clouds).

tomobear • Science 67%

TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.

awesome-rlaif • Science 54%

A continually updated list of literature on Reinforcement Learning from AI Feedback (RLAIF)

evolution-by-emergence • Science 67%

LaTeX source of the open‑access book “Evolution by Emergence” on networks, complexity & universal evolution (CC‑BY).

https://github.com/bioinfo-pf-curie/mpibwa • Science 13%

https://github.com/bimberlab/nimble • Science 36%

nimble — execute lightweight, flexible alignments on custom reference libraries

https://github.com/bimberlab/nimble-aligner • Science 26%

nimble-aligner is the backend for nimble, a tool that executes lightweight, flexible alignments to generate supplemental alignment data

bioinformatics-toolbox • Science 57%

Docker container for bioinformatics tools and pipelines

amino_align • Science 18%

Python code for bioinformatics about proteins

wally • Science 49%

Wally: Visualization of aligned sequencing reads and contigs

bamtocov • Science 67%

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

dpo-rlhf-paraphrase-types • Science 67%

Enhancing paraphrase-type generation using Direct Preference Optimization (DPO) and Reinforcement Learning from Human Feedback (RLHF), with large-scale HPC support. This project aligns model outputs to human-ranked data for robust, safety-focused NLP.

subaligner • Science 67%

Automatically synchronize and translate subtitles, or create new ones by transcribing, using pre-trained DNNs, Forced Alignments and Transformers. https://subaligner.readthedocs.io/

https://github.com/broadinstitute/celligner2 • Science 36%

A new version of the celligner package using VAEs. Inspired from the Theis lab's scArches.

symbolic-governed-mistral-artifact • Science 44%

Tier-10 sealed governance artifact for Mistral-7B with exact-match benchmarks and symbolic verifier.

cath-tools • Science 28%

Protein structure comparison tools such as SSAP and SNAP