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

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

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

BMEB Thesis project which develops ssDNA aptamer sequences from probabilistic data per provided protein epitope.

This program determines the optimal alignment of two nucleotide sequences using the Smith–Waterman algorithm. Optimality, of course, is determined by the values of the gap penalty g and the weight matrix (that lists all of the s(ai , bj )). Finally the program outputs the optimal similarity score along with the optimal alignment.