RAxML or BV-BRC tree

Question

[anna]

Hello everyone,

I am doing a phylogenetic analysis on some strains isolated and downloaded from ncbi to have a validated tree to use in an article. I am proceeding using two systems. Before I used the BV-BRC tool for building trees. I then tried to do the alignment with progressiveMAUVE (BV-BRC tool), and then I analyzed the alignment with RAxML to build the bootstrap tree and the best tree. so I’ve viewed them both with iTOL. This is the first time I have done this analysis and I do not know which system is correct.

Hope someone will help me.

A.