Boot strap - Urgent (Apr/11/2007 )

Hai there all,

Im writting my thesis. Im doin phylogenetic analysis. Would like to ask wht is a boot strap sequence. How to get tht programme. Pls do help me out!!!

thanks

Hey, bootstrapping is where the program will make small random changes in your sequence alignment, then see if your phylogenetic branches are still the same, ie it's testing to see how 'robust' your phylogenetic tree is. It's common to use 100 or 1000 bootstrap cycles, that why you will see phylogenetic trees with numbers on them, the number is how many times out of 100/1000 that branch occurred (hope that makes some sense). One such program is Seqboot, it's part of the PHYLIP group of programs, I am not sure if it's freely available, I used to use it off the ANGIS server, but that requires a (hefty) subscription.
More information here - http://evolution.genetics.washington.edu/p...oc/seqboot.html

You should try the online programs from Pasteur institute

http://bioweb.pasteur.fr/seqanal/phylogeny/intro-uk.html

It do bootstrap automatically for the method choosed like NJ, ML, UPGMA etc..

hi,
try this....its a link to phylip software

http://evolution.genetics.washington.edu/phylip.html

I have also used SEQBOOT and CONSENSE for bootstrapping. u might like to give it a try as well.