I want to construct a phylogenetic tree based on 5 housekeeping loci from two different Vibrio spp. Reviewing the literature, it is a generally accepted practice that the 5 loci are concatenated before multiple sequence alignments. After multiple sequence alignments it is also show that alignment trimming is performed in order to remove necessary gaps and regions that are not conserved. I have found an alignment trimming tool called trimal . I was wondering if anyone has used this and why would it not be better to simply use a program like MEGA and use the complete-deletion option where sites missing data or alignments gaps are removed before phylogenetic tree construction? Isn't the option in MEGA essentially the same thing as trimming?.. what are the benefits and drawbacks of both? Any help would be appreciated Thanks.