Cladistic and phenetic analyses of RFLP data

Yves Bertheau bertheau at inapv.inapg.inra.fr
Mon Dec 14 07:18:48 EST 1992


Dear netters,

We are comparing several Erwinia bacteria by RFLP (rRNA) or RFLP after
specific PCR (on the amplified fragments of genes involved in pathogenicity)

We plan to make phenetic and cladistic analyses of the data:

1) Does somebody know a good review about the analysis of RFLP data using
a phenetic approach (the several similarity indices, the distances...), I
know for the cladistic approach several papers by J. Felsenstein, are they
other of the same type?

2) Are we allowed to analyze PCR/RFLP data as classical RFLP data? Or is a
new approach necessary for the RFLP data originating from amplified fragments?
(phenetic and cladistic approaches)

3) We used 4 and 6 bases cutters restriction enzymes. How could we analyze the
data with the Nei and Li distance when we know that the number of nucleotides
is a part of the formula? Do we have to make separate analysis depending on the
number of nucleotides recognized by the enzymes?

4) Same question as in item 3 when using the PHYLIP package, what to do when
we used 4 and 6 bases cutters?

Thanks in advance

-- 

		Yves Bertheau
		INRA INA P-G
		Pathologie Vegetale
		16 rue Claude Bernard
		75231 Paris cedex 05
		FRANCE
Phone: +33 (1) 43.31.93.97	Fax  : +33 (1) 43.31.83.82
Telex: 250985			Internet bertheau at inapv.inapg.inra.fr

-- 
		Yves Bertheau
INRA INA P-G		Pathologie Vegetale	16 rue Claude Bernard	
75231 PARIS cedex 05	FRANCE	Tel +33 (1) 43.31.93.97 
Fax: +33 (1) 43.31.83.82 Internet: bertheau at inapg.inra.fr



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