AntonPetrov

awesome-rna-3D-tools

awesome tools for RNA

pyaln

Read, process, write multiple sequence alignments

qjob

Utility to split shell commands into jobs, then submit them for computation to a queue of a SGE or Slurm cluster.

DesiRNA

State of the art software for RNA sequence design. The first to solve the Eterna benchmark!

spqr

Simulation code for the prediction of RNA structures.

learna_tools

A command line interface to the generative RNA design approaches LEARNA, Meta-LEARNA, Meta-LEARNA-Adapt and libLEARNA.

pxblat

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

usearch12

Open-source usearch

msabrowser

🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations

react-msaview

A multiple sequence alignment viewer

rich-msa

A Rich renderable for viewing Multiple Sequence Alignments in the terminal.

docker-circos

Docker image for Circos

txtools

An R package to process and analyze transcriptomic data

puter

🌐 The Internet OS! Free, Open-Source, and Self-Hostable.

CREDOengine

Coronavirus_SL5_3D

Accompanying the publication: Tertiary folds of the SL5 RNA from the 5’ proximal region of SARS-CoV-2 and related coronaviruses

bioframe

Genomic interval operations on Pandas DataFrames

RNA-Undesign

Undesignability of RNA secondary structures

Ribovision_2.0_GT

py-rcsbsearchapi

Python interface for the RCSB PDB search API.

FMAlign2

FMAlign2: A novel fast multiple nucleotide sequence alignment method for ultra-long datasets

bpRNA

bpRNA: Large-scale Annotation and Analysis of RNA Secondary Structure

JSAV

JavaScript Sequence Alignment Viewer

Prop3D

A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cleaned" domain structure in CATH.

MBDBMetrics

MBDBMetrics: An online metrics tool to measure the impact of biological data resources

pipettor

robust, easy to use Python package for running Unix process pipelines

EternaFold

Improving RNA structure prediction through multitask learning on diverse crowdsourced data.

r2dt-client

npysearch

Python bindings for the nsearch library (https://github.com/stevschmid/nsearch)

RNAsselem

a Python package for descriptive analysis of RNA secondary structure elements in viral genomes