676 Open source projects that are alternatives of or similar to Biopython

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Single-Cell Analysis in Python. Scales to >1M cells.

Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.

compacted de Bruijn graph construction in low memory

WebLogo 3: Sequence Logos redrawn

MISO: An open-source LIMS for NGS sequencing centres

Python module for average nucleotide identity analyses

A full spaCy pipeline and models for scientific/biomedical documents.

🌈Scaffold genome sequence assemblies using linked read sequencing data

Syntax highlighting for computational biology

Estimate metagenomic coverage and sequence diversity

🐣 locally query the ncbi taxonomy

A simplified pipeline for ctDNA sequencing data analysis

A friendly next-generation interface for Genomic data discovery powered by InterMine

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

Fast multi-line FASTA/Q reader in several programming languages

Genome inference from a population reference graph

Toolset for SV simulation, comparison and filtering

Javascript full-stack framework for Big Data visualisation and analysis

Parser and database to index the terpene profile of different strains of Cannabis from online databases

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

No description or website provided.

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

An open-source toolkit for large-scale genomic analysis

A Practical and Efficient NCBI Taxonomy Toolkit

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

A wrapper for the EnsEMBL REST API

📊 Identify cell types and pathways affected by genetic risk loci.

A library for generating an interactive SVG visualization of CWL workflows

variant expressions, annotation, and filtering for great good.

Fast & accurate alignment of barcoded short-reads

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

SortMeRNA: next-generation sequence filtering and alignment tool

(No maintenance) Detect gene fusion directly from raw fastq files

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

ECG classification programs based on ML/DL methods

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Emperor a tool for the analysis and visualization of large microbial ecology datasets

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Yet Another Chimeric Read Detector

Introduction to the Unix Shell for biologists

Guided synteny alignment between duplicated genomes (within specified quota constraint)

😴 📂 Create and Query a Local Copy of GenBank in R

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

(formerly eelpond) an automated RNA-Seq workflow system

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

A Suite of Packages for Analysis of Big Genomic Data

The sources of the openSNP website

Simulate genealogical trees and genomic sequence data using population genetic models

JAMP - Just Another Metabarcoding Pipeline

highly-efficient & lightweight mutation signature matrix aggregation

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

an implementation of NSGA-II in java