Extracting transcripts from whole-transcriptome libraries

Hi there,

I am having trouble finding a tool that will successfully extract specific transcripts from whole transcriptome libraries. The transcriptome libraries were assembled through Trinity, and the reference transcriptome was a de novo assembly from Trinity also.

My ultimate goal is to extract the transcripts of interest, and then compare SNP counts and calculate dN/dS ratios. Any help is appreciated! Thanks.