Is it possible to introduce mutations (SNV/Indels) in precomputed lastz alignments

Question

[Saad Khan]

Hi,

I have multiple resequencing files from multiple species that I am trying to compare. For each individual vcf file I generate a alternate fasta using FastaAlternateReferenceMaker. I was wondering if there is a tool/package that can introduce the mutations (indel/snv) in the precomputed alignment last files without having to re do the lastz alignments for multiple alternate fasta files.

Thanks!