ToolsStudents at Arc

Central to Arc’s mission is not only developing state-of-the-art technologies, but also making them widely available to accelerate biomedical research across the globe. At Arc’s Tools Portal, we’re sharing our growing list of computational tools developed by Arc scientists, along with supporting publications, documentation, and code. 

Check back often, as we’ll be posting new tools as they are launched, and feel free to contact us at with any questions.

Software & Tools

Algorithms, software, analysis pipelines, and machine learning models to extract new insights, accelerate discovery, predict biological outcomes, and visualize results.

Machine Learning Tools

Evo: DNA Foundation Model

Evo is a biological foundation model capable of generative design from molecular to genome scale at single-nucleotide resolution.
Preprint, February 2024

Genome Engineering Tools

Bridge RNA Design Tool

This tool designs bridge RNA sequences for recombining user-defined target and donor DNA sites using the IS621 bridge recombination system.
Perry et al., Nature, 2024

Cas13d Guide Design Tool

Built from the largest Cas13d knockdown dataset to date, Arc's deep learning-powered Cas13d Guide RNA Selection Tool nominates high-efficiency guide sequences and any custom RNA sequences for knocking down your transcript of interest across human, mouse, other model organisms, and custom sequences.
Wei et al,. Cell Systems, 2023


ScreenPro2 is a tool for flexible pooled CRISPR screen analysis.

Gene Expression Tools

APAlog: Statistical Framework for Analysis of Differential Poly-Adenylation

Analysis of alternative poly-A site selection and processing using 3‘-end RNA sequencing.
Nature Cell Biology, May 2023

pyteiser: Modular Implementation of TEISER in Python

Discovery of RNA structural elements using in silico and hybrid RNA SHAPE strategies.
Science, May 2021

RiboLog: A Statistical Framework for Ribo-Seq Data Analysis

Ribosome footprinting pre-processing, QC, and analysis.
Nature Cell Biology, May 2023

SwitchFinder: Computational Discovery of RNA Structural Switches

A tool designed for the systematic discovery of RNA structural switches within transcriptomes.
Nature Methods, July 2024


RBP Browser: RNA-binding protein map

A shiny app for exploration of the Goodarzi lab’s RBP post-transcriptional regulatory modules.
Preprint, March 2023