Dear all,
I would like to know how to combine two or more DNA barcode sequences in one phylogenetic tree. Do you combine all sequences first to make one long stretch of sequence and align it with others (that you make in the same way?). Thank you.
Hi Trina:
I did not know if you were writing about different contigs of a same gene or fragments of different genes. Looking at your profile I saw that you are working with DNA barcodes of plants using multiple loci, so I assume your question is about using more than one gene to generate a single phylogeny.
If this is the case, yes, concatenation ("make one long stretch of sequence") of your gene sequences is one option. However, the most important step is to align each gene independently, and later concatenate the aligned sequences. The result of this concatenation of multiple genes will be a matrix that can be analyzed using your preferred phylogenetic method(s).
You can easily concatenate your sequences using the program Sequence Matrix, available here: http://www.ggvaidya.com/taxondna/
I hope it helps!
Yes, it's concatenation, but one has to be careful when different markers have radically different evolutionary scenarios. The resulting tree should be interpreted with caution.
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