pcca : a program for phylogenetic canonical correlation analysis
This program uses a PGLS transformation to obtain transformed data and then performs canonical correlation analysis on the phylogenetic transformed data. It can also estimate Pagel's (1999) λ and use the multivariate MLE of λ in the phylogenetic transform. Download the zipped tarball (recommended) pcca.tar.gz, which includes a detailed manual, example files, Linux binary, Mac OS X binary, and windows executable. The pcca manual is also available here, as are the pcca Windows executable, Mac OS X binary, and pcca Linux binary.
Reference:
Revell, L. J. and A. S. Harrison. 2008. PCCA: A program for phylogenetic canonical correlation analysis. Bioinformatics 24: 1018-1020. PDF
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IDC : a program for the calculation of independent contrasts
This simple program calculates independent contrasts as well as a variance-covariance matrix and correlation matrix of independent contrasts for quantitative trait data and a phylogeny. It can handle multiple data sets and/or trees. Download the zipped tarball IDC, which includes manual, example files, binary, windows executable, and source. The IDC manual is also available here.
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T_method : a program for Roff's T-method
of matrix comparison
T_method is temporarily unavailable until I fix a silly error which seriously affects the calculation of P-values from the permutation test.
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skewers : a program for Cheverud's random skewers method
of matrix comparison
This program calculates the mean random skewers vector correlations for the comparison of two or more variance-covariance matrices from phenotypic, genetic, or other data. This approach is based on Cheverud et al. (1983) and especially Cheverud (1996). Download the source (skewers.c) or a DOS/Windows executable (skewers.exe). A zipped tarball with all relevant files is also available, skewers.tar.gz, as is a short manual.
Important update: I fixed a bug found on Sept. 10, 2006. Please replace any earlier versions.
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multi_mantel : a program for multiple matrix regression and hypothesis testing
This program performs a multiple matrix regression for a single dependent correlation or distance matrix and an arbitrary number of independent matrices. It performs hypothesis testing of the multiple regression by permuting rows and columns together in the dependent matrix, following the Mantel permutation procedure (Mantel 1967). This program performs an analysis similar to that which I believe is available in Passage, a program which also performs many other types of analyses. This program, however, returns an output, including an ANOVA and t-table as well as predicted and residual matrices, that will look very familiar to biologists used to performing similar analyses with typical (non-matrix) data. Download the source (multi_mantel.c) or a DOS/Windows executable (multi_mantel.exe). A zipped tarball with the multi_mantel manual, all executables and source code, and an example input file is also available (multi_mantel.tar.gz).
A helpful complementary program is distance, the source code of which is available here (distance.c) along with a DOS/Windows executable (distance.exe). Distance calculates the pairwise Euclidean distance among all possible pairs of points and returns an output that can be readily adapted for input into multi_mantel. Distance is very simple to use, reading an input file in the following format (input.txt). Another similar program, but for calculating patristic distances from a phylogenetic tree in the form of tree.txt, is patristic.exe.
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