Tools
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 tools@arcinstitute.org with any questions.
Software & Tools
Machine Learning Tools
State is a multi-scale AI model that uniquely operates on sets of cells to capture population-level and cell-level perturbation effects using a modern transformer architecture.
State Preprint
Evo 2 is a biological foundation model capable of generative design from molecular to genome scale at single-nucleotide resolution.
Evo 2 Preprint
Evo 1 Published November 2024, Science
SynGenome is a first-of-its-kind database consisting of synthetic DNA sequences generated by Evo, a genomic language model. Given a DNA sequence prompt, Evo will generate a DNA sequence response that continues the genomic sequence. Essentially, Evo enables "autocomplete" for the genome.
Genome Engineering Tools
Given 14 bp target and donor sequences and a bridge RNA scaffold, this tool will return the sequence of candidate bridge RNAs that should work with the respective bridge recombinase.
Perry et al., Nature, 2024
Perry et al., Science, 2025
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
iAnalyzer is an analytical pipeline designed for the robust analysis of CRISPR screens. It streamlines the processing of CRISPR screening data, facilitating tasks such as quality control, alignment, and statistical analysis to identify significant genetic perturbations.
Cell Reports, September 2024
Gene Expression Tools
Analysis of alternative poly-A site selection and processing using 3‘-end RNA sequencing.
Nature Cell Biology, May 2023
Discovery of RNA structural elements using in silico and hybrid RNA SHAPE strategies.
Science, May 2021
Ribosome footprinting pre-processing, QC, and analysis.
Nature Cell Biology, May 2023
A tool designed for the systematic discovery of RNA structural switches within transcriptomes.
Nature Methods, July 2024
Analytical Tools
Bioinformatics Tools
BINSEQ is a family of simple binary formats that enable high-performance parallel processing of sequencing data.
Preprint, April 2025
A performant and storage-efficient CLI tool to extract sequences from an SRA archive with support for FASTA, FASTQ, and BINSEQ outputs.
Atlases
Curated collection of single cell transcriptomic data from over 200 million cells.
A shiny app for exploration of the Goodarzi lab’s RBP post-transcriptional regulatory modules.
Nature Communications, September 2024