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Cazin Antoine edited this page Jul 13, 2026 · 3 revisions

Sequence Analyzer Toolbox

The Sequence Analyzer Toolbox is a bioinformatics tool for identifying genotypes and predicting pathogenicity from nucleotide sequences. It compares input sequences against a curated reference database and, when configured, analyzes a defined cleavage or virulence site region.

The tool supports any pathogen for which you can provide:

  • A reference FASTA database with correctly formatted headers
  • Optionally, a cleavage site position and a motif classification file

Features

  • Genotype identification: similarity-based matching against a reference database (Hamming or Pairwise)
  • Multi-gene support: analyze multiple gene segments simultaneously and combine genotypes (e.g. H5N1 from HA + NA)
  • Pathogenicity prediction: cleavage site motif analysis across 3 reading frames
  • Phylogenetic trees: placement of query sequences among reference neighbours (FastTree or IQ-TREE2)
  • Database statistics: genotype distribution, temporal trends, host and geographic coverage
  • Precision validation: repeated holdout accuracy testing against the reference dataset

Tools Used

  • MAFFT: Katoh et al. - multiple sequence alignment
  • FastTree: Price et al. (2009/2010), PLOS ONE - approximate maximum-likelihood trees
  • IQ-TREE2: Minh et al. (2020), MBE - full ML trees with ModelFinder + ultrafast bootstrap

Developed as part of a bioinformatics internship project
Source: https://github.com/Soupirr/NDV-genotyper

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