I was working with a set of DNA sequences (1026 bp each) for phylogenetic analysis. STRUCTURE software package is widely used for PCoA as known to me. But I don't know how to use sequence data for software feed and the format (to which and how sequence data could be converted). can anyone lead me to the step by step procedure for the analysis? (thanks in advance)
[P.S.: I had gone through the software website and user guide, so please don't mention that one]
http://web.stanford.edu/group/pritchardlab/structure.html
Pritchard's STRUCTURE is not PCOA but clustering technique, and it requires multilocus nuclear data. To perform ordination analysis of your data, you can calculate matrix of dissimilarity indexes (e.g. Fst i.g. in Arlequin) and import it into PAST (https://folk.uio.no/ohammer/past/). PAST is a simple and user friendly program. Principal Coordinates Analysis could be performed with PAST. But first try MDS.
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