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

Protein Alignment and Detection Interface

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

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

Benchmark the performance of sequence alignment workflows

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

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

compleasm genome coverage analysis using awk

genome and transcriptome alignment extraction

stitching coding regions from exon alignments for the protein to genome alignments.

maf alignments from protein to genome alignments using awk

miniprot protein alignment analyzer

miniprot protein analyzer

protein alignment gem from alignment to graphs

intergenic region analyzer from protein alignments to draft genomes.