I have an alignment of about 40 proteins from marine invertebrates. I'd like to build a tree based on this alignment. I've used RAxML, but was wondering if there were other tree building software that were better suited for gene trees, specifically.
In my experience the most important part of the tree is to make it easily interpreted and point out your "key points" to them through visualization. As you are only testing 40 genes i would look into there variability and possibly find something similar or known to root your tree to. Other wise small or large SNPs (even poor vs good quality sequencing) will cause a lot of issues. No alignment algorithm can fix that.
You can generate the tree file using BEAST, EPA, HYPHY, PAML, PHYLDOG, pplacer, r8s, RAxML or RevBayes, whever you are comfortable using then visualize in ggtree. ggtree has the same idea as ggplot so it is easy to manipulate, color or structure for the best appearance. If you are not a fan of R like some of my collogues they really enjoy using iTOL.
Keep in mind that phylogenetic trees depend very much on the alignment method as well. This is not a problem if you are using sequences that exhibit low divergence, but can be quite tricky for highly divergent ones.
Almost any phylogenetic software can produce a gene tree. I can recommend ExaBayes (if you have a long alignment with many taxa), or MrBayes for smaller datasets.