Molecular phylogenetics

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

Niche modeling and GIS

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

Other

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