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.

ProTrek: illuminating the Protein Universe through Trimodal Protein Language Model (Connecting text and protein)

Open-source usearch

Protein Alignment and Detection Interface

SSAlign

OTalign: Protein sequence alignment for remote homologs using Protein Language Models and Unbalanced Optimal Transport.

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

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

Protein alignment using gap penalty traceback with the Blosum62 Matrix

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

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

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.

JavaScript implementation of Needleman-Wunsch algorithm for global alignment, hosted on GitHub Pages!

Benchmark the performance of sequence alignment workflows

Benchmarking 6 MSA tools (Clustal Omega, MUSCLE, MAGUS, M-Coffee, MSA Probs, MSA Transformer) across BAliBASE, OXBench & PREFAB datasets.

A custom progressive Multiple Sequence Alignment (MSA) algorithm for Hemoglobin β protein evolution analysis using Needleman-Wunsch alignment, BLOSUM62 scoring, UPGMA guide trees, and comparison with Clustal Omega.

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