I am a sophomore who is majoring in biology, and completely new to bioinformatics . I was tasked with searching for Aeromonas in a metagenome. I used bowtie2 to align reads from next-gen sequencing of the metagenome to a FASTA of gryA subunit of two different Aeromonas(ran separate alignments for both). My professor now wants me to create a phylogenetic tree using my results. At the risk of sounding dumb, how do I do this? I created a visual of the alignment using IGV but I'm not sure what software to use to create a phylogeny or even how to go about it in any way.I saw that Mega 7 can create a tree, I've also used Seaview, but how would a create a tree using the files and results I have(Sam,Bam,BAI,) Any help would be greatly appreciated.
