Comprehensive programs

These are comprehensive programs that perform many types of operations needed in geometric morphometrics..

MorphoJ The MorphoJ program package provides a platform for a wide range of analyses in geometric morphometrics. The program is written for both 2D and 3D data, with some inevitable differences in the graphical output possibilities etc. MorphoJ is available for free under the Apache License, Version 2.0.

Features presently implemented in the program include: -- Procrustes fit for 2D and 3D data with and without object symmetry -- Import/export of data sets and supplementary information -- Identification of outliers (with choices for including/excluding observations and fixing some problems) -- Generating covariance matrices ('standard' and pooled within-group covariances) -- Principal component analysis -- Matrix correlation (including automatic adjustment for symmetry/asymmetry for configurations with object symmetry) -- Two-block partial least squares -- Regression (arbitrary numbers of dependent and independent variables; also pooled within-group regression, e.g. for allometry correction in multiple groups) -- Canonical variate analysis -- Linear discriminant analysis, including cross-validation -- Mapping shape variables onto a phylogeny -- Various analyses concerning the quantitative genetics of shape and selection for shape

Additional features will be included in future releases.

The software is written in Java, and includes external libraries that are also written in Java. As a result, the program is more or less platform-independent. At the moment, there are distributions of the test versions for Windows, Macintosh OS X (10.4 Tiger and higher) and Unix/Linux (tested under Ubuntu Linux only). All what you will need to run it is a recent Java Runtime Environment (minimum Version 5.0) for your operating system, which is available for free from (Windows and Unix/Linux) or comes with your operating system (Mac; users of Tiger may have to upgrade to version 5.0).

Further information and links for downloads and documentation of the software are available from: The following link may also be helpful: Guide for new users of MorphoJ

Morphologika2 Morphologika is a free program for the analysis of 3d coordinate data. It offers GPA and PCA of tangent space coordinates and allows ready visualisation of results. Online documentation is available from the download link. For more information contact Paul O'higgins. Version 2.5 12/7/08
MODICOS Computes Euclidean distances and centroid size (CS) from a set of coordinates x,y and use CS to estimate heritabilities and Qst. It also computes relative warps and uniform components of shape variation from a set of coordinates x,y and use any relative warp or uniform component to estimate heritabilities and Qst's. For Windows 95+. By A. Carvajal-Rodríguez. To install the program, unzip the file and execute setup.exe. Readme file. 1/21/04
Morpheus et al.

Cross-platform package for morphometric data analysis. Versions for AIX, DOS/WIN, LINUX, and SGI. Provides a comprehensive, cross-platform environment for the acquisition, processing, and analysis of morphometric data. Download from the Morpheus final beta website Link to the new morpheus at By Dennis E. Slice.

Integrated Morphometrics Package for Windows. The six programs that can be downloaded from the link given at the left. CoordGen6 - Generates a variety of different types of shape coordinates, and translates files back and forth between the IMP file format (called X1Y1) and the TPS file format used by the tps series of programs. This program is the entry point into IMP. It also produces reference forms for thin plate spline analysis. This is the "entry point" into the IMP system. PCAGen6- Principal Components Analysis for geometric morphometric data. The program computes Partial Warp plus Uniform component scores, based on the Thin Plate Spline decomposition of the deformation, and then displays the deformations implied by various loadings of PCA Axes. CVAGen6 - This is a Canonical Variates Analysis program for landmark data. The program computes the Partial Warp plus uniform component scores and then does the CVA on these scores. Determines the set of axes that best discriminates among groups, along with the statistics related to those axes. A tool for classifying groups.

Regress6 - A multipurpose program, producing thin plate spline deformation (partial warp) scores, and regressing them on a dependent variable, typically centroid size. It also computes Procrustes distances from a reference, and calculates the associated statistics. Tmorphgen6 - Generates a set of traditional morphometric variables (lengths) from a geometric morphometrics data set. TwoGroup6 - Carries out pairwise tests of significant differences in shapes between groups, using Goodall's F-test and Hotelling's T2 test, in addition to bootstrap versions of these tests. The program also computes the Partial Procrustes distances between the means of the groups.

The "moreIMP" site provides links to updates and two new programs.

Developed by David Sheets

Morphometrika Morphometrika. Mac PowerPC. Download from author's website.  
PAST Palaeontological Statistics package for Windows, including morphometrics and multivariate statistics. Integrated program with e.g. thin-plate splines, PCA, Procrustes fitting, partial warps, Hotelling's T^2, discriminant analysis, multidimensional scaling, cluster analysis, elliptic Fourier and eigenshapes. By Oyvind Hammer. Download at 6/6/02

Last modified on August 19, 2015 by F. James Rohlf ( ).
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