TreeGradients Phylogenetic tree drawing program using color or grayscale gradients to trace continuous characters along the tree.
	PMT – Partitioned Model Tester Facilitates selecting partitioning strategies and models of sequence evolution for phylogenetics.
	gDAM – graphical Data Availability Matrix Program that draws a graphical representation of data availability in a concatenated sequence alignment.
	TF-pipe – TreeFinder pipeline Pipeline to accelerate TreeFinder analyses manifold by running parallel jobs on clusters (Sun Grid Engine).
	Phran Phran performs quality control on sequence chromatograms (using Phred) and adds the quality-checked sequences to a reference alignment.
	SiteStripper Perl script to 'site strip' alignments, i.e. remove a given percentage of fast-evolving sites.

	MMS – Maxent Model Surveyor Program that evaluates predictor sets and model complexity for Maxent using AIC, BIC or test AUC.
	OccurrenceThinner Performs distance-based thinning of species occurrence data to reduce geographic sampling bias in niche modeling.
	RasterTools A set of Java tools for raster and vector GIS applications commonly needed in niche modeling studies.
	Bio-ORACLE A comprehensive and user-friendly dataset of GIS rasters for the marine realm, designed for global niche modeling applications.

MatrixGradients Program to visualize a continuous variable in a matrix using color or grayscale gradients.