How to create a phylogenetic tree

Question

[anna]

Hello everybody,

I’m trying to build a phylogenetic tree with the Galaxy RAxML tool. I ran the multi genomes alignment with MAUVE but can’t figure out what input Galaxy tool want and where to find it on MAUVE.

I hope you can help me,

Anna

[Joe]

Please use more informative tags - they are supposed to help group and identify posts so that people can more readily find the posts they're interested in or can help with.

AFAIK Mauve doesn't generally do an alignment in the typical sense of the word - it is usually moving contigs around to obtain the most similar assemblies.

There currently aren't any really good/scalable ways to align multiple full genomes (unless they are very small, and even then you'll encounter limitations).

It would be helpful if you explain more about the data you're working with and what you are hoping to achieve.