This is the repository for the PAP-DPB2 Phylogenetic analysis project.

Waste Management for Captain of Industry game

COI sequences files used to test the COI Classifier Web Portal

Back up for the review and scripts used in the article "The evolutionary outcomes of climate-change-induced hybridization in insect populations." published in COIS,

This repository contains the scripts used to process Illumina MiSeq 18S, ITS2, and CO1 metabarcodes for Jesse Hoage's Master's thesis (2018). The ammended CO1 reference set is also included here (CO1 Classifier v2.1).

Data flow to process COI metabarcodes

NuclearPlus mod for CoI

Datasets and code used to create figures in "Hajibabaei et al., 2019. COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems. PLoS ONE 14(9): e0220953."

MalariaGEN Plasmodium falciparum Community Project analysis using coiaf

Unpowered Balancers for Captain of Industry game

An R Shiny application to identify cochineal genetic sequences for 12S rRNA, 18S rRNA, or COI.

ČOI adblock list

Datasets and code used to create figures in "Hajibabaei et al., 2019. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS ONE 14(12): e0225409."

CoI debugging in vscode

A python script that makes it easy to analyze multiple COIs (Communities of Interest) and generate heat maps and metrics of interest.

PipeCraft2 is a Graphical User Interface (GUI) for various metabarcoding pipelines

Captain of Industry mod.

Complexity of Infection Estimation with Allele Frequencies

Snakemake bioinformatic pipeline to process COI mtDNA metabarcodes

A set of Xcode file templates to use when developing on OX Coi