Reverse Dependencies of biopython

The following projects have a declared dependency on biopython:

• 3dstrudel — Strudel package
• A2G — Accurarate amplicon alignment to gene consensus
• ab12phylo — Integrated pipeline for ML phylogenetic inference from ABI trace and FASTA data
• abdesign — Antibody humanization framework
• abmap — AbMAP: Antibody Mutagenesis Augmented Processing
• abutils — Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
• academicdb — Database for an academic CV
• acdc-nn — A deep learning predictor of protein stability change upon mutation
• acppred — Screening anticancer peptide from amino acid sequence data
• adams — this is a program for fast protein structure search
• agfusion — Python package to annotate and visualize gene fusions.
• aideml — Autonomous AI for Data Science and Machine Learning
• aimap — aimap provides a package and script for finding the modification from Adenosine to inosine (A to I).
• aimhii — A pipeline for mapping insertion mutants from whole genome shotgun data
• aims-immune — A software for the analysis of immune repertoires
• aiondata — A common data access layer for AI-driven drug discovery.
• airpg — A package to automatically access the inverted repeats of archived plastid genomes
• albatradis — Comparitive transposon mutagenesis experiment analysis
• aleph — ALEPH is a bioinformatics tool for structure interpretation and generation of fragment-based library for Molecular Replacement.
• algn2pheno — A bioinformatics tool for rapid screening of genetic features (nt or aa changes) potentially linked to specific phenotypes
• alifedata-phyloinformatics-convert — alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data
• alignme — Alignment Tool based on Biopython
• allcools — Toolkit for single-cell DNA methylome and multiomic data analysis.
• allcopol — AllCoPol: Inferring allele co-ancestry in polyploids
• alpha2fasta — Encode text written in natural language in a FASTA-based format
• alphabase — An infrastructure Python package of the AlphaX ecosystem
• alphabetsoup — tile phylogenetic space with subtrees
• alphafold — An implementation of the inference pipeline of AlphaFold v2.0.This is a completely new model that was entered as AlphaFold2 in CASP14 and published in Nature.
• alphafold-colabfold — An implementation of the inference pipeline of AlphaFold v2.3.1. This is a completely new model that was entered as AlphaFold2 in CASP14 and published in Nature. This package contains patches for colabfold.
• alphafold-kagglefold — An implementation of the inference pipeline of AlphaFold v2.0.This is a completely new model that was entered as AlphaFold2 in CASP14 and published in Nature. This package contains patches for kagglefold
• alphafold2-pytorch — AlphaFold2 - Pytorch
• alphapulldown — Pipeline allows massive screening using alphafold
• alphascreen — Use colabfold to screen protein-protein interactions.
• alv — A console-based sequence alignment viewer
• AmberPy — A tool for setting up and performing molecular dynamics simulations using Amber on the University of Leeds Arc HPC
• ambie — AMBIE: Assessment of Metagenome BInnErs
• aMGSIM — aMGSIM: simulate ancient metagenomes for multiple synthetic communities
• aminocode — The aminocode library can be used to encode texts written in natural language in a format based on amino acids
• AminoExtract — AminoExtract is an application to extract aminoacid sequences from a fasta file based on a GFF.
• AMIVA-F — no summary
• AMPcombi — A parsing tool for AMP tools.
• amphipathic — This is a library to evaluate an aminoacid sequence and determine an amphipathic index for each alpha helix or beta sheet.
• AmpliSeek — AmpliSeq amplicon mapper tool
• amptk — AMPtk: amplicon tool kit
• ancient-helper-kit — helper functions to be used in a pipeline for virus discovery
• Angua-Luggage — no summary
• ankh — Optimized Protein Language Model
• annofetch — Command Line Script to fetch annotations.
• ANNOgesic — ANNOgesic - A tool for bacterial/archaeal RNA-Seq based genome annotations
• annonex2embl — Converts an annotated DNA multi-sequence alignment (in NEXUS format) to an EMBL flatfile for submission to ENA via the Webin-CLI submission tool
• annoPipeline — API-enabled Gene Annotation
• AnnotationPipeline — WUR nematology Annotation Pipeline
• anospp-analysis — ANOSPP data analysis
• ANTIPASTI — Deep Learning model that predicts the binding affinity of antibodies from their three-dimensional structure.
• anvage — toolkit to process routine operation on gff3, vcf and fasta files
• apollo — Apollo API library
• apollo-sdk — A radically simple framework for ML/AI model management
• approximate-cluster-identities — A package to calculate and visualise approximate cluster identities for a large number of short nucleotide sequences using minimizers.
• appsquared — Antigenic Prediction for Protein Sequences Pipeline
• apscale — Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data
• apscale-gui — Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
• aqbt — Aquarium strain builder tools
• arbow — Cultivate your MSA to get better trees
• arcimboldo — a suite of programs for x-ray diffraction structure solution
• arctic3d — Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
• ariba — ARIBA: Antibiotic Resistance Identification By Assembly
• armadillin — Lineage prediction from SARS-CoV-2 sequences
• arraylib-solve — Tool to computationally deconvolve combinatorially pooled arrayed random mutagenesis libraries
• atligator — Atlas based editing of protein interactions
• atom3 — 3D Atomic Data Processing
• atom3-py3 — 3D Atomic Data Processing (Python 3 version)
• atom3d — ATOM3D: Tasks On Molecules in 3 Dimensions
• austrakka — A CLI to interact with AusTrakka
• autocbei — "autoCBEI.py" can calculate the potential CBEI loci of the target CDSs and perform statistics and plots.
• automlsa2 — Automated Multi-Locus Sequence Analysis tool
• autopacmen-Paulocracy — The AutoPACMEN package
• aviary-genome — aviary - metagenomics pipeline using long and short reads
• azulejo — tile phylogenetic space with subtrees
• b2constsites — Generate an appropriate data tag to add constant sites to your BEAST2 XML
• bacpacs — Bacterial Pathogenicity Classification via Sparse-SVM
• bacpage — An easy-to-use pipeline for the assembly and analysis of bacterial genomes
• bact-order — Author: J.Iszatt
• BacterialTyper — no summary
• bad-phylo — Tool for the estimation of the difficulty of phylogenetic placements
• badlon — A bioinf tool for analyzing pan-genome and other features based on synteny blocks
• bakta — Bakta: rapid & standardized annotation of bacterial genomes, MAGs & plasmids
• bam2tensor — Bam2Tensor
• bamdash — create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
• bandwagon — Simulate DNA band patterns for gel migration experiments
• bandwitch — Enzyme selection for DNA verification and identification
• BanzaiDB — Database for Banzai NGS pipeline tool
• BarcodeFinder — All-in-one solution for discovering novel DNA barcode
• basicsynbio — An open-source Python package to facilitate BASIC DNA Assembly workflows
• BayesASE — Bayesian analysis of allele specific expression
• bcbio-gff — Read and write Generic Feature Format (GFF) with Biopython integration.
• BdRPCpackage — Phylogenetic new sample placement software.
• beastify — Partition your alignment into distinct codon positions and non-coding positions
• beditor — A computational workflow for designing libraries of guide RNAs for CRISPR base editing
• BFG-Y2H — Analysis scripts for BFG-Y2H data
• bfscan — bfscan is designed to detect foodborne pathogens using bloom filter and machine learning