I am working on horizontal gene transfer (HGT), and as part of my pipeline, making phylogenetic tree. I am using MAFFT for creating the alignment (MSA) and RAxML for tree building. As the analysis is to see if there is transfer of a gene from a distant clade, there are lot of ambiguities in the actual alignment, such as lot's of GAPs. One common approach is to delete/remove the GAPs (to reduce noise) using automated tools like Gblocks, trimAL.
However, I came across this paper today: Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference https://www.ncbi.nlm.nih.gov/pubmed/26031838
So, what should I do now? This paper is well debated, spent more than four years under peer-review process. Interested people can read this blog: http://lab.dessimoz.org/blog/2015/08/27/filtering-alignments