Dear All, thank you for your time. I have a dataset containing 15,000 sequences. I wish to build a tree and thus my plan was to use BlastClust, a module in the Blast application to cluster them, then use a reference sequence from each cluster to build a crude tree. BlastClust has been running for some time now but I have no idea whether this is going to work or how long it will take.
I was wondering if there are any other ways of going about this with a such a large set of sequences?
Ideally, I wanted to be able to do a sequence alignment and then use that alignment of build a tree (which I agree will be complex with that number of sequences) and then look at the evolution of those sequences.
I tried something called MAFFT to do the sequence alignment, which did not give me any errors but gave me no output.
Any suggestions would be appreciated.