MycoAITaxoTagger, 2025
A Deep Learning and Semantic Search based classifier for DNA Barcode Identification
Github: TaxoTaggerhttps://github.com/MycoAI/TaxoTagger
Github:taxotagger-webapphttps://github.com/MycoAI/taxotagger-webapp
MycoAI, 2024
A software package, written in Python, for exploring various AI models including MycoAI-CNN and MycoAI-BERT for (fungal) eDNA identification.
Dnabarcoder’s web-interface, 2023
Dnabarcoder, 2022
A software package for computing similarity cut-offs for different (fungal) clades and for classifying eDNA sequences
Github: dnabarcoderhttps://github.com/vuthuyduong/dnabarcoder
WI SNP variant calling, 2021
A pipeline for SNP variant calling, using whole genome sequencing
Github: SNPanalysishttps://github.com/vuthuyduong/SNPanalysis
This pipeline was listed in the following community paper comparing the 14 pipelines developed by different labs around the world for SNP variant calling analysis:
Deep learning based fungal classifiers, 2020
A framework for applying the deep learning models including Convolutional Neural Networks (CNN) and Deep Belief Networks (DBN) for fungal classification, and comparing the outputs with traditional methods suchs as BLAST and RDP
Github: fungiclassifiershttps://github.com/vuthuyduong/fungiclassifiers
Fast Multi-Level Clustering, 2018
fMLC is the official implementation of the MultiLevel Clustering (MLC) algorithm decribed in Vu D. et al.(2014), used to cluster massive DNA sequences. It is written in C++ and supports multi-threaded parallelism. fMLC is also integrated with an interactive web-based tool called DIVE to visualize the resulting DNA sequences based embeddings in 2D or 3D. The work is financially supported by the Westerdijk Fungal Biodiversity Institute and the Netherlands eScience Center.