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bootstrapping - to do or not to do (Aug/30/2005 )

I have sequenced the 16S 23S region of my organism I have about 20 strains and would like to comparem them with each onther and other known strains from Genbank.
The problem is my bootsrap values are 6, 7, 9, 11, 65, 50 ant others.
Does this mean my branch lengthes are too short and I should assume that they should all be on the same part of the tree.
Should I bootstrap at all?

Any suggesstions PLEASE!!!!!!!!!!!!!!!!!!!!


As with my understanding, bootstrap numbers indicate how similar the sequences are. For example, if A and B are in the closet node, the bootstrap number 900 for this node would mean that out of 1000 calculations, 900 times, A and B would appear in the closet node. The numbers you are giving are way too low. Generally numbers that are lower than 800 should not be counted.
What program are you using to do the N-J tree?


I am using MEGA to draw my trees.
Jukes and cantor model, all site are equal.
I believe the values are percentages, i agree they are low. is there anyway to increase the values, changing th e number of replicates does not help. They are the same organism.
could it be the presence of N's in the sequences?


A question: are you referring to the Intergenic Transcribed Spacer 16S->23S or to the two separate genes of 16S AND 23S?
The alignment topic is totally different in the two cases.