I am interested in constructing a phylogenetic tree on 30 viruses using their respective DNA polymerase sequences. The problem is that the sequences vary in length and are not as similar as one may think even though the viruses are related. is there a recommended method/program that will get around this problem? I am also interested in using a chimera of the viral DNA pol and the major capsid protein for the tree.
If you have highly divergent sequences it is most recommended that you asses for substitutional saturation. Once that has been asessed you can determine if your DNA sequences hold any true phylogenetic signal rather than inferring erroneous relationships.
This can be done in a software package called DAMBE
For highly diverged sequences, you could also try to translate them into protein sequences, and then align with MEGA, it may elevate the accuracy of gap alignment.
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