As jrj.healey said, yes, this is feasible to be done, but we would need more information about the dataset you have to provide more detailed answers.

One pipeline for phylogenomics analyses is Agalma. From the paper:

Each phylogenomic study requires many steps, the vast majority of which concern matrix construction rather than phylogenetic analysis itself. These steps include raw data filtering, assembly, identification of ribosomal RNA, selection of transcript splice variants, translation, identification of homologous sequences, identification of orthologous sequences, sequence alignment, phylogenetic analysis, and summary of results.

It is geared towards transcriptomic raw data, but it has facilities to introduce pre-assembled transcripts / genes.