MORPHOMETRICS, STATISTICS, SIMULATION SITES:

Imaging Software:

• FIJI - Version of ImageJ with preloaded plugins.
• Base ImageJ - Software for processing and editing images
• StereoMorph - R package to digitize landmarks and generate 3D images from multiple 2D pictures.
• WinDig - Software for digitizing points on electronic files

Random Number Generators:

• Random.org - Program for generating random numbers

Geometric Morphometrics Software:

• Morphometrics at Stony Brook- Comprehensive guide to geometric morphometrics software. For individual programs, I recommend the tps series developed by Jim Rohlf at Stony Brook. See:
• tpsDIG2 - Program to digitize landmarks on digital images
• tpsRelw - Program that performs procrustes superimposition and principal component analysis (PCA) of landmark data
• tpsRegr - Program that performs procrustes superimposition and regression analysis of landmark data
• tpsSplin - Program to visually compare pairs of specimens using deformation grids (thin-plate spline)
• tpsPLS - Program that performs a partial least-squares analysis to explore the covariance between a set of variables and variation in shape or between two shapes
• tpsUtil - Utility program for tps software

Other Geometric Morphometrics Software:

• GeoMorph - R package for geometric morphometrics
• Geometric Morphometrics Tools Package
• IMP-Integrated Morphometrics Software
• Morpheus et al.
• MorphoJ- Geometric Morphometrics software
• Morphologika
• SlicerMorph Project

3D Morphological Analysis / Micro-CT Scanning:

• 3D Slicer
• SlicerMorph Project
• SlicerMorph bioRxiv Article
• SlicerMorph Tutorials

Online Geometric Morphometrics Books:

• Guia Practica de Morfometria Geometrica - ResearchGate link to PDF guide on Geometric Morphometrics in Spanish.

Online Statistics and Quantitative Analysis Books:

• Analisis Multivariado para Datos Biologicos - Teoria y Su Aplicacion Utilizando R - ResearchGate link to PDF book on Multivariate Analysis in Spanish.

Statistics:

• Past- Free Statistical Software Program
• VassarStats-Wonderful online statistics package

R Links, Tutorials, and Books:

• The R Project for Statistical Computing
• R Studio- Interface for using R.
• R Tutorial- An Online R Tutorial.
• Learning R- PDF of book by Ricard Cotton.
• Modern Statistics with R. Online book by Mans Thulin.
• Modern Statistics for Modern Biology. Online book on Statistics in R and Bioconductor by Susan Holmes and Wolfgang Huber.
• R for Data Science- Online version of book by Wickham & Grolemund.
• R Graphics Cookbook- Online version of book by Winston Chang.
• R Markdown- R Markdown: The Definitive Guide by Yihui Xie, J. J. Allaire, Garrett Grolemund.
• Beyond Multiple Linear Regression. Applied Generalized Linear Models and Multilevel Models in R. Online book by Paul Roback and Julie Legler.

Population Dynamics & Simulation Software:

• Populus- Simluations of Population Biology.

Last Updated April 26, 2022.