Unistrap is a method designed to generate boostrap replicates that takes into account MSA instability and guide tree effects. Unistrap can use most third party aligners and guide tree estimators.
The final publication can be accessed from pubmed.
A powerpoint is available here.
Please Cite:Chatzou M, Floden EW, Di Tommaso P, Gascuel O, Notredame C. Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty. Syst Biol. 2018 Nov 1;67(6):997-1009. doi: 10.1093/sysbio/syx096pubmed