likelihood and indels

Gerald M. Schneeweiss gerald.schneeweiss at UNIVIE.AC.AT
Mon Apr 14 11:33:44 CDT 2003

I am wondering what is happening in programs such as PAUP or
MrBayes, when you feed them with a matrix of aligned sequences
including indels: Are those columns excluded from the calculations or
do they lead to spurious results?

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