dna-barcoding

A Go package for engineering organisms.

High-performance dual barcode and primer demultiplexer for MinION sequenced reads, optimized for fungal DNA barcoding.

An R package for pre-processing and error evaluation of COI-5P barcode data

Automated DNA barcoding pipeline: chromatogram → phylogeny → species ID. Zero coding required. Built for ENTM201L @ UC Riverside. Docker + GitHub Classroom ready.

This repository contains data and code from the manuscript, "Analysis of biodiversity data suggests that species are hidden in predictable places".

Parser of BLAST results

Pipeline for building topologically-constrained phylogenies from DNA barcode data

DNA barcoding analysis pipeline

My first DNA barcoding project - Philippine Eagle, Barn Owl, and Sumatran Rhinoceros

Tools for managing OTU definitions for barcoding fungi

A sequence-by-sequence denoiser for COI DNA barcode and metabarcode data

Files from DIMACS 2007 DNA barcoding challenge

DNA barcode-based aquatic species classification using canonical k-mer frequencies and RandomForest. 96% top-1 accuracy on 2,100+ species.

Bioinformatic processes used to obtain invertebrate DNA barcodes from Illumina sequencing output

Iterative extrapolation of species haplotype accumulation curves for genetic diversity assessment.

R package for extracting chloroplast DNA barcode markers from GenBank plastomes, including rbcL, matK, and psbA-trnH.

Nanopore-based amplicon pipeline for Anopheles species identification using COX1 and ITS2 consensus sequencing

Ophelia – An interactive forensic investigation game featuring molecular analysis (FASTA sequence), DNA markers, and fingerprint analysis to solve crime cases, built using Java GUI with NetBeans frame navigation.

A bioinformatics pipeline that enables DNA barcode classification using a novel strobemer based profile hidden markov model (sPHMM) method.

Mediterranean fish species ID from COI sequences. SVM matches BLAST at ~100x speed. Includes interpretability probe.