In order to construct phylogenetic trees, we make comparisons between sets of genes belonging to different taxa. We are working under the assumption that the taxa we are studying are related by evolution. Therefore, we need to ensure that the genes we use to construct our trees are orthologous - that is, they have evolved through speciation events, from a common ancestor.OMA Groups are groups of sequences that are all orthologous to one another, and can be found in the OMA Browser. See the OMA Group module for more details.
In order to construct phylogenetic trees, we must first align the sequences. This allows us to compare sequences site by site. There are a multitude of Multiple Sequence Alignment (MSA) tools available, many of which can be found on the EBI website here.
Alternatively, you can try the alignment and tree inference tools available online at www.phylogeny.fr (in particular PhyML) or an IQTree webserver here, as an alternative to RAxML if the queue is too long at Vital-IT.
Now that we have our trees, we would like to visualise and compare them. Unfortunately, the output format (Newick) isn't particularly conducive to interpreting trees. Thankfully, there are online viewers such as phylo.io to help us.