Bootstrapping a neighbor joining tree w/Phylip?

Fredj Tekaia tekaia at pasteur.fr
Mon Jun 28 05:46:49 EST 1993


In article <20c9onINN5r3 at s-crim1.dl.ac.uk> mbfw at s-crim1.dl.ac.uk
(Frank Wright)
 writes:
>Robert Rumpf asked about bootstrapping phylogenetic trees using
>the PHYLIP package....
>
>The PHYLIP package allows you to bootstrap trees constructed using
>any of the tree construction methods (including Fitch-Margoliash,
>Neighbor-Joining, Parsimony).  The basic idea is that you create
>many shuffled datasets by running SEQBOOT, then run the tree construction
>method of your choice, and then run the CONSENSE program to get the
>final bootstrapped tree.
....
>     SEQBOOT, then DNADIST and NEIGHBOR, then CONSENSE
......
>     SEQBOOT, then DNAPARS, then CONSENSE
.....
>     SEQBOOT, then PROTDIST and NEIGHBOR, then CONSENSE
.....
>     SEQBOOT, then PROTPARS, then CONSENSE
........


 A side issues of this presentation is :
 can someone point to papers synthetizing in which conditions might be
 used each of these tree making techniques? 
Having aligned sequences, which are the criteria that suggest the choice
of one or more of these techniques? In which limits might the results
be comparable?

Thank you

 Fredj Tekaia

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