Rhagoletis pomonella - apple maggot fly (H Robertson, Univ. Cephus cinctus - wheat stem sawfly (H Robertson, Univ. Zea mays - maize re-annotation (C Lawrence, MaizeGDP). Oryza sativa - rice re-annotation (R Buell, MSU). Diabrotica virgifera - corn rootworm beetle (H Robertson, Univ. parasitic nematode genomes (M Mitreva, Washington Univ). Lactuca sativa - Lettuce (RW Michelmore) - Annotation in progress. Cronartium quercuum - rust fungus (JM Davis, Univ. Arabidopsis thale cress re-annotation (E Huala, TAIR) - Manuscript in preparation. Nannochloropsis - micro algae (SH Shiu, Michigan State Univ.) PubMed. Latimeria menadoensis - african coelacanth () - PubMed. Megachile routundata alfalfa leafcutter bee () - Manuscript in preparation. Columba livia - pigeon (M Shapiro, Univ. Cardiocondyla obscurior - tramp ant (J Gadau, Arizona State Univ.) - Manuscript in preparation. Fusarium circinatum - pine pitch canker (B Wingfield, Univ. Petromyzon marinus - Sea lamprey (W Li, Michigan State) PubMed. Conus bullatus - cone snail (B Olivera Univ. Pogonomyrmex barbatus - red harvester Ant (J Gadau, Arizona State Univ.) PubMed. Linepithema humile - Argentine ant (CD Smith, San Francisco State Univ.) PubMed. Atta cephalotes - leaf-cutter ant (C Currie, Univ. Pinus taeda - Loblolly pine (A Stambolia-Kovach, Univ. Pythium ultimum oomycete (R Buell, Michigan State Univ.) PubMed. Schmidtea mediterranea - planaria (A Alvarado, Stowers Institute) PubMed. 
MAKER has been used in many genome annotation projects: MAKER can be used for de novo annotation of newly sequenced genomes, for updating existing annotations to reflect new evidence, or just to combine annotations, evidence, and quality control statistics for use with other GMOD programs like GBrowse, JBrowse, Chado, and Apollo.
However, MAKER is also designed to be scalable and is thus appropriate for projects of any size including use by large sequence centers. MAKER is an easy-to-use genome annotation pipeline designed for small research groups with little bioinformatics experience. 9.8 User Interface for Local MAKER Instalation.9.5 Improving Annotation Quality with MAKER's AED score.9.1.8 External Application Behavior Options.9.1.2 Re-annotation Using MAKER Derived GFF3.9 Advanced MAKER Configuration, Re-annotation Options, and Improving Annotation Quality.6.6 Selecting and Revising the Final Gene Model.6.5 Integrating Evidence to Synthesize Annotations.6 Details of What is Going on Inside of MAKER.3.4 Comparison of Algorithm Performance on Model vs.3.2 What sets MAKER apart from other tools ( ab initio gene predictors etc.)?.2.3 Effect of NextGen Sequencing on the Annotation Process.
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