Research article
Constructing a meaningful evolutionary average at the phylogenetic center of mass
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* Corresponding author: Eric A Stone eric_stone@ncsu.edu
1 Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695-7566, USA
2 Department of Statistics, North Carolina State University, Raleigh, NC 27695-8203, USA
3 Department of Pathology, Stanford University, Stanford, CA 94305-5324, USA
4 Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
BMC Bioinformatics 2007, 8:222 doi:10.1186/1471-2105-8-222
Published: 26 June 2007Additional files
Additional file 1:
Two phylogenetic covariance matrices. (a) The ACL covariance matrix Σ under the Brownian motion model for the phylogeny in Figure 5a. The weights in Figure 5b are proportional to 1TΣ-1. (b) The effective covariance matrix Eτ[Στ] used by BranchManager for the same phylogeny. The weights in Figure 5b are proportional to 1T(Eτ[Στ])-1.
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Additional file 2:
Standardized versions of the four physicochemical property scales used in the text. These scales were used in conjunction with the alignment data in Figure 5c to create Figure 6.
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Additional file 3:
An implementation of the BranchManager in the statistical language R.
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