These projects and others are available in my GitHub repositories.

Simulation tools

VPGsim - Generates a population of virtual ferns with configurable genetics in a 3D environment

VPCsim - Simulates a plant community with configurable habitat in a 3D environment

Bioinformatics tools

gbs-tools - A set of tools for evaluating the quality of Genotyping-by-sequencing datasets

gb2tbl - Converts a genbank genome flat file to a features table for importing into Sequin

muscletrans - Takes fasta format dna sequence and performs translation alignment using MUSCLE

findprimer - Searches for shared primer sites in distantly related taxa

conservedmsats - Searches for shared microsatellites in distantly related taxa

PECS - Classifies putative edit sites found by comparing genome sequence with transcriptome data

Miscellaneous tools

diversitydb - Stores and visualizes plant species diversity data collected by middle school students as part of the ISIT project

Wolf-Tracking-Tools - Batch converts wolf tracking data to a format that can be viewed in Google Earth/Maps

Opensimulator region modules - Experimental add-on modules for the Opensimulator 3D server to log chat and visitors and to demonstrate cellular automata