advice on bootstrapping values

Mike Tennant tennant at mh.uk.sbphrd.com
Thu Mar 19 12:08:06 EST 1998


Hi,
    I have a protein multiple sequence alignment of some very divergent
sequences (245 sequences altogether), generated using PSI-BLAST from
ncbi. This alignment contains quite a lot of gap regions (I'd estimate
that about well over 50% of the positions have gaps characters in), but
the core regions are all aligned in a sensible manner. I've bootstrapped
the resulting tree (1000 samples) in clustalw, and seen that the values
on the nodes in the sub-trees (those sequences which are easily related)
are relatively high (80+ %), but the values between sub-trees can be
very low (as low as 2%).
    I'd appreciate it of anybody could comment on these values,
especially as to whether they are meaningless or not. Any other advice
on tree creation when one's MSA contains lots of gaps would also be
welcome.

thanks in advance!

--
Mike.






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