Yes, I think that you should consider using MultiSeq which is a package of Visual Molecular Dynamics (VMD). You can use visual molecular dynamics to make phylogenetic trees based on sequence/structural/other statistical means.
If you want to check it out and see if it works for you, then install visual molecular dynamics: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
and try out these tutorials under Bioinformatics from the distributors:
Note: VMD doesn't work very well in 64-bit Windows operating systems if that's what you use. To get it to work well, I suggest you install virtualbox from Oracle, and install your favorite free open-source Linux operating system into virtualbox or into your guest linux machine on your host machine.
I suggest installing your guest Linux OS on virtualbox with 1/2 the ram of your host physical computer allocated, and like 100 GB of space for when you discover that you love LINUX so much and have lots of information on there.
To full-screen your guest Linux OS, you need to install guest additions.
My favorite Linux OS is Kali Linux.
To install guest additions on Kali Linux and most linux guests on VirtualBox,
you have to do this:
But as I've discovered you have to upgrade Kali Linux to Kali Linux Rolling to get Kali Linux to fullscreen. How you do that is via this:
And you probably shouldn't do your work as user "root" the default user. You have too much power so to increase security create a new user on Kali-Linux:
If you are already using linux, then you won't have any problem with getting VMD to work. But by the way, you have to install VMD from the command terminal in linux and this is how you do it.
The instructions as for how this guy does it (and sorry he doesn't speak English) are in the README file when you download VMD.
Sorry, apparently, I don't have a high enough reputation to cite you all the links. I'm sorry that I had to remove them.