I want to construct a phylogenetic tree using the maximum likelihood method and the phylogenetic tree will be constructed based on the gene. But I am not sure whether to use the DNA sequences or protein sequences. Which one should I be using? When do I use DNA sequences and when do I use protein sequences when constructing a phylogenetic tree?
Dear Agnes,
You can use either. Typically if alignment of DNA sequences (i.e. you know they are homologous, but the sequence difference is great) is hard you may change to amino acid sequences (e.g. in viral genes). Comparing both results is not wrong. Usually though DNA based sequences are used. Good luck!
Sometimes protein sequences are nice because the variation at the 3rd position in not an issue. On the other other hand 3rd position sites can be quite phylogenetically informative.
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