I would like to take PFGE profiles (and possibily also ribotypes and
PCR-RFLP patterns) of different strains of the same organism, and
generated with several different restriction enzymes, and combine the
data to produce a phenetic (phylogenetic) tree.
For the PFGE profiles neither the location of the cutting sites nor
the precise number of sites can be known. Thus, RESTML cannot be
used as it assumes that the sites are mapped. Is this correct?
Therefore, I propose to use the equation of Nei and Lei (PNAS 76: 5269,1979)
D = 1 - 2(n(xy))/(n(x)/n(y)) as described by Vilgalys and Hester (J Bact 172:
4238, 1990) and Gurtler et al (J Gen Microbiol 137: 2673, 1991).
In this approach the individual distance matrices of D values are averaged
to produce a single matrix for e.g. FITCH. Is this valid?
Are there other (better) ways of approaching this problem?
Virus Reference Division
Central Public Health Laboratory
61 Colindale Avenue
London NW9 5HT
Phone: + 44 (0) 181 200 4400 ext 3245
Fax: + 44 (0) 181 200 1569
Email: jclewley at hgmp.mrc.ac.uk