|Manual comparison||minimal overhead||extremely tedious; error prone; unscalable|
|Genome browser||intuitive interface; visual assessment of individual loci||visual assessments imprecise; extensive overhead; little or no automation|
|Eval||detailed statistics; visual assessment of statistic distributions; scales fairly well for large data sets; can compare multiple predictions to a single reference||older software; relatively slow; only summary statistics are reported, while stats for individual loci are discarded|
|ParsEval||detailed statistics provided, not only as a summary but for individual loci as well; scales well for large data sets; fast, efficient, and portable||only capable of comparing a single pair of annotations|
Various approaches to comparing alternative sources of gene structure annotations, with a brief description of the associated pros and cons.