Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

Open-source usearch

ProTrek: Navigating the Protein Universe through Tri-Modal Contrastive Learning

Protein Alignment and Detection Interface

Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc

Protein alignment using gap penalty traceback with the Blosum62 Matrix

FASTA Alignment search for BsaI and BsmBI restriction sites in the ORF6 protein to verify assertions made by Bruttel, et. al. in "Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2."

Flexible protein alignment using Protein Units

Implementation of the Combinatorial Extension (cealign) algorithm to align protein structures

This project applies bioinformatics techniques to analyze biological sequences, including protein structure prediction, sequence alignment, and comparative genomics using tools like BLASTP, AlphaFold3, and BioPython. It combines algorithmic methods with practical applications in computational genomics.

MutFold | Human breast cancer associated mutant protein structure prediction and alignment application

Benchmark the performance of sequence alignment workflows

For viewing, analyzing, and generating figures of protein sequence alignments.