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Two-letter country codes indicating the origins of the viruses included in the envelope tree in Fig. 1 are as follows: Malawi (MW), Burundi (BU), Ethiopia (ET), Brazil (BR), Central African Republic (CF), Thailand (TH), Uganda (UG), Kenya (KE), Rwanda (RW), Zaire (ZR), United States (US), Australia (AU), France (FR), and Haiti (HT).
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FastDNAml and DNArates were written by Gary Olsen and colleagues at the Ribosomal Database Project (RDP) at the University of Illinois at Urbana-Champaign
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To create this tree, we generated a preliminary maximum likelihood tree which was then used as input for the DNArates program (47) that produced the maximum likelihood estimate of the rate of nucleotide substitution at every position in the alignment, allowing nine categories of rates. The preliminary tree and rates and categories were used to create a new tree, allowing global rearrangements and adjusting of branch lengths. Maximum likelihood was used to generate the tree to get the most accurate branch lengths possible (9, 11). It took 3 weeks of computer time on a SPARC workstation to generate this tree, so bootstrap analysis was done by using the neighbor joining package of Phylip with the maximum likelihood model to calculate the genetic distances (43).
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We thank C. Kuiken, T. Leitner, K. Rock, and B. Foley for helpful discussions, R. Thakallapally and A. Ploss for their help with the preparation of this manuscript, and P. Ginsparg for suggestions concerning the text. B.K. was supported by interagency agreements between the U.S. Department of Energy (DOE) and NIH, 3-Y01-AI-70001-13 and Y1-A1-4058-03; J.T. by the DOE; and S.M.W. by grants RO1 -HD-31756 and PO1 -AI-42454 from NIH, and a gift from an anonymous foundation.
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