It would be way easier for me to construct your trees than provide the information you would need to make a good tree. Could probably do it is a day if it is aligned or 2 if no using maximum likelihood methods which are the most robust, least biased of all methods.

I teach tree-building over 14 or 15 lectures in an advanced undergrad/grad student course. If you have a good alignment you could plug it into any number of programs but you will not know if your method is good or exactly what the tree(s) shows. Choosing the right method, the right model and the right way to evaluate your results is not a trivial task.

Let me know if you'd like some help.

Thank you! I would love some help. Right now, I have an undergraduate working on it as her Capstone senior project, but will eventually publish it, giving you credit (co-authorship, if you wish). Right now she only has the COI and 12S data. Later I will add 16S. That might mean making the tree twice (one with 12S and COI, then with all three), so if that is too much of a waste, we can wait and just do the single tree for the publication. Thanks and let me know how to proceed, if you are willing.

Actually I would advise doing single trees from each "gene" and then concatenating them with a separate model for each gene for a final tree. I am guessing that the COI will be the more informative of the three. Making a tree twice or more is not a problem. I could also include a blow by blow description of the methodology that I use and what she should use for the future. Knowing some phylogenetic technique should help her with her future career.

you can check the following link. there's a method to build phylogenetic tree from multiple sequences.

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