I saw this plot in Allen KD, McKernan K, Pauli C, Roe J, Torres A, et al. (2019) Genomic characterization of the complete terpene synthase gene family from Cannabis sativa. PLOS ONE 14(9): e0222363. https://doi.org/10.1371/journal.pone.0222363, and it goes

Gene models for 53 substantially complete terpene synthases (manually curated by combining Exonerate and StringTie outputs) are shown in Fig 7.

Next these queries were used to estimate gene models using Exonerate operating in exhaustive mode on the gene region. (Exonerate version 2.2.0, [19]). This gave a set of protein similarity based gene models that were often full length, but due to relatively low levels of conservation in the first exon (particularly when a targetting signal is present) some models were missing part of the first coding exon. Where possible gene models were manually adjusted based on the transcriptome data to yield complete gene structures.

I think it only mentioned the alignment step, not the visualization...? Thank you!