I have generated transcriptomes from my focal species and its outgroup. I want to now find out what is the ancestral state at some sites based on the outgroup. How do people usually accomplish this? The easiest way to do this would be to map the outgroup reads to the focal species transcriptome but I am worried about diminished sensitivity due to lower mapping rate. The other option is to align orthologous contigs from the both transcriptomes and find out the position of interest in the outgroup from the alignment, and then see if there is a SNP in this position in the VCF file but it seems hard to automate?