MSA: Gene Family annotation

Question

[Dillon]

I am interested in understanding and knowing which sequence alignment would be the best for genome wide analysis of an gene family, I see that maximum likelihood is used mostly but I am just curious if anyone on here knows of more optimal ways of sequence alignment?

ps. i understand that i could just google it and understand how alignment works (global vs local) but i want to get comfortable with blogging and building up a network of people who are interested in bioinformatics and optimizing methods for analysis, thank you