MESPA

MESPA is a python based pipeline that builds gene models from fragmented genome assemblies. 

The identification of genomic regions underlying phenotypic differences is central to many questions in evolutionary biology. These studies involve the generation of a high-quality genome and annotation, which consumes a considerable amount of resources in terms of time, money, and personnel. However, most of the causal variation is found in or near genes, so having good gene models is essential. We believe MESPA will aid in circumventing the limitations of the traditional approach by allowing the use of fragmented, low-quality assemblies to build good gene models based on protein sequences from a closely related species.

Manual: https://sourceforge.net/p/mespa/wiki/Manual/
Tutorial: https://sourceforge.net/p/mespa/wiki/Tutorial/