[Mauve-users] Calculating a "real" whle genome pyhlogenetic tree using mauveAligner

[<mic...@ag...>]

I am looking for a way to generate a phylogenetic tree of 30 pseudomonas strains by using mauve. Since the guidetree outputted by progressiveMauve is not a "real" phylogenetic tree I am looking for another "whole genome approach".

Would it be an option to generate a phylogenetic tree the following way?:
1. Get FastA file form 30 strains and concatenate into one file
2. Align them with command: mauveAligner --output=ps.mauve.phylip --output-alignment=ps.alignment.phylip --weight=300 --alignment-output-format=phylip --alignment-output-dir=. ../ inp/all/all.fasta
3. Use raxml or fastree on the phylip which gets generated by mauveAligner

Thx
Michael