I have not heard of issr or NTYSIS, but I have a guess at what your problem is and can offer a simple possible solution.

My guess at what your problem is... The result of a single throw at your analysis is a complicated structure...like a dendogram.

So if I do bootstrap replicates, how do I combine them?The answer is that you need to refine the question you're trying to answer. So you 

1. Have a dataset

2. You have done an analysis resulting in dendogram(s)

3. You have results based upon this analysis.

Now why are you doing bootstrap? I'm guessing it's for addressing the reliability of your answer.  Are talking 1st order bootstrap i.e. your estimating the classification error, ir are you talking 2nd order ...You want something akin to a confidence interval or a p-value 

In order to proceed you should first decide what the ultimate result is. My guess is that it's a small handful of summary statistics...the correct classification rate? An importance measure for one or more of the predictors?

The explicit answers depend. Can you provide more detail?

Dear Grant Izmirlian

thanks for your answer

i am comparing two molecular system (ISSR and SCoT) in tomato species.

in these to molecular systems, i have two trees (dendrograms) that dose not have bootstrap values. i made these trees by NTsis free software that have ability to calculate some values such as genetic similarity, PCA, PIC, RP and others.

i have to calculate bootstrap values in my trees but i do not know how to calculate them for my data. My data is on 0 and 1 sheet format in the excel file.

so please help me to do this by any software you propose.

thanks.