Conclusion
Genome annotation, especially in medium to low quality drafts of non-model organisms, is still a drawback for the increasingly large number of evolutionary and functional genomic analyses in the context of molecular ecology studies. To assists this task, we developed a comprehensive pipeline that facilitates the curation of existing models and the identification of new gene family copies in genome assemblies. The improved annotations generated with this pipeline can be used directly to perform downstream analyses or as a baseline for further manual curation in genomic annotation editors. Future directions should include the possibility of including novel sources of evidence in BITACORA searches, such as RNA-seq data, or the integration of the pipeline as a part of genome annotation editors to facilitate gene family annotation in collaborative genome projects.