Hello. I am trying to use microsatellites to make a phylogenetic tree using Mr.Bayes. However, if I am reading correctly, I need to code my alleles as morphological data and it looks like I can only use the numbers 0 through 9, yet I have 22 alleles in one marker. Is there another way?
Dear Heather
Maybe you have a choice to make Ten groups of alleles ( in the case of nearly similar morphology), and then give numbers within each group for an individual allele, I do not sure that idea will be suitable.
I hope the following link will be useful for you:
http://bioinformatics.oxfordjournals.org/content/17/8/754.full.pdf+html
Good Luck
Try indel coding! You need to align these SSRs according to Kelchner 2000, then do indel coding following Simmons & Ochoterena 2000 (e.g. in Seqstat http://bioinfweb.info/Software/SeqState). You can use the output directly in PAUP for ML analysis or convert it in TreeGraph2 (http://treegraph.bioinfweb.info/) to a combined dena/binary matrix and use it as input to mrbayes/raxml etc.
http://sysbio.oxfordjournals.org/content/49/2/369.full.pdf
Hi, actually microsatellite data does not reflect phylogeny. I would suggest try distance based tree such as neigbor-joining tree.
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