I would like to better understand the pipeline for building a phylogenetic tree of a gene's evolution across species (whose genomes have been sequenced). What would be the appropriate procedures and software?
I am inexperienced at bioinformatics, and assume it would go something like this:
1) Elicit the gene sequence
2) BLAST the gene sequence to find homologs in other species
3) Build phylogenetic tree
I am trying to determine how three genes (cgMT1, cgMT2, MTF1) evolved across three types of coral. These genes are shown in humans to reduce injury from heavy metal exposure. My tentative hypothesis is that in the one type of coral (of the three) that is most sensitive to bleaching (prone to lose its symbiosis with dinoflagellates due to UV, pollution, and heavy metal exposure), there will either be an absence of one or more of these genes or a distinct evolutionary history that may have rendered these genes dysfunctional.
However, I do not even know how to elicit the gene sequences (cgMT1, cgMT2, MTF1) from human databases and/or one of these species and/or all species, and compare between the species. I am very lost about how to start, and just would like to develop a short and simple (beginner-level) pipeline to test this hypothesis. I would like this pipeline to be entirely computational.
I know this is a fairly open-ended question (and may not make sense), so please understand that I am new but have really given myself a headache. Thank you for any advice!