Post-quantum cryptography migration just got its first enforceable federal deadline. EO 14409 requires U.S. agencies to ...

pggb builds pangenome variation graphs from a set of input sequences. A pangenome variation graph is a kind of generic multiple sequence alignment. It lets us understand any kind of sequence variation ...

Abstract: In this study, we design a hardware accelerator for a widely used sequence alignment algorithm, the basic local alignment search tool for proteins (BLASTP). The architecture of the proposed ...

This script works with Python 3, it takes as input a VCF file and will use the SNP genotypes to create a matrix for phylogenetic analysis in the PHYLIP (relaxed version), FASTA, NEXUS, or binary NEXUS ...

This important study addresses the problem of detecting weak similarity between protein sequences, a procedure commonly used to infer homology or assign putative functions to uncharacterized proteins.

In 2022, a team of computer scientists presented a groundbreaking algorithm for the maximum flow problem: How does one transport the most supplies from a source node to a sink node in a network while ...

Proteinortho is a widely used tool to predict (co)-orthologous groups of genes for any set of species. It finds application in comparative and functional genomics, phylogenomics, and evolutionary ...

Edit distance—a classical problem in computer science—has received ongoing attention from both practitioners and theoreticians. Given two strings A and B, the edit distance is the minimum number of ...

SNAP is a program that is part of a gene sequencing pipeline. It takes data from gene sequencing hardware that consists of short chunks of DNA (typically 70-300 base pairs long) called reads and ...

NeighborNet constructs phylogenetic networks to visualize distance data. It is a popular method used in a wide range of applications. While several studies have investigated its mathematical features, ...

Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61081, United States Department of Bioengineering, University of Illinois ...