bootstrap values

Sarah Tamara Braun brauns at rpi.edu
Mon Feb 12 05:54:53 EST 1996


In Article <311F024E.5D29 at mbla.ucl.ac.be>, Moulliard Charles
<moulliard at mbla.ucl.ac.be> wrote:

>I have made 1000 bootstaps using SEQBOOT and then calculate the most 
>parsimonious tree with DNAPARS. But, when I look to the tree, I don't see 
>the bootstraps value. How can I see on the postscript tree file the 
>bootstrap values. 

After DNA pars, you need to run Consense.exe to generate the consensus
tree for all the values.  The bootstrap data is in the outfile. You should
then run DNAPARS and generate one tree from the entire sequence, and add
the bootstrap values to that tree. 

>What is the best way to analyse the data and to find the tree?
>
>DNA parsimonious <-> DNA branch and bound algorythm <-> Maximum likelihood 
>analyses <-> ... ?
>

Generally, it is a good idea to do both a Parsimony tree and a distance
tree (both bootstrapped) and then compare the two. Hopefully they
should be similar...

Hope that helps!!

Cheers,


       Sarah Tamara Braun

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