I am interested in extracting multiple species alignment for a subset of species included in the UCSC multiz100way whole genome alignment. My GTF file contains exons, but ultimately I'd like to stitch together the full length transcripts and obtain FASTA formatted alignments for each transcript.
Does anyone know which tools I can use to do this?
My current plan is to use PHAST tools like msa_split to obtain the MAF of just there regions and species of interest but then I'm not sure how to recover transcripts. Any thoughts or suggestions are welcome!