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Background: I have Hackett 2009 (from birdtree.org) phylogenetic tree and I need to reorder it according to Prum 2015. I also work only with some species relevant to my project, not the entire tree.


I currently use Mesquite, and it is absolute purgatory. Doing any reordering in Mesquite takes insane amount of time. I'd also like to add higher taxon information to each species (like order) to help my my orientation in the data. I understand some of Mesquite's shortcomings might be shortcomings of Nexus format. As I don't need to analyse the data myself, I can work in some better format like PhyloXML as long as it's possible to export back to Nexus format in the end.

Is there any way to do this? Some software with better visual editor (and overall better UX) or other method to do this in effective manner? I find it hard to believe that much bigger data is handled in such clumsy way.

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  • $\begingroup$ Can you just start with the Prum tree and cut it down to your taxa? $\endgroup$ – kmm Oct 16 '16 at 3:29
  • $\begingroup$ If one of the answers is helpful for you, it would be a nice gesture towards the author to accept it. Additionally the system will not bump the question anymore. $\endgroup$ – Chris Dec 15 '16 at 19:43
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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:

http://www.ks.uiuc.edu/Training/Tutorials/

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.

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I had good experiences with Archaeopteryx. This is a java package so it should be easy to run but I recommend the BioLinux if you don't want to spend too much time installing and get straight to the biology. You can run it as a virtual machine or install it side by side. It is getting a bit older but everything works just out of the box and there is a wide array of tree editing tools installed. Just look through the package list.

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