The paper introduces MAKER, a portable and easily configurable genome annotation pipeline designed to facilitate the annotation of eukaryotic genomes and the creation of genome databases. MAKER identifies repeats, aligns ESTs and proteins to the genome, produces ab initio gene predictions, and integrates these data into gene annotations with evidence-based quality indices. The pipeline is highly customizable and trainable, allowing for the improvement of gene models through retraining. MAKER's outputs are compatible with the Generic Model Organism Database (GMOD) format, enabling direct integration into GMOD browsers and databases. The authors demonstrate MAKER's effectiveness by annotating the genome of the planarian *Schmidtea mediterranea* and creating a new genome database, SmedGD. They also compare MAKER's performance with other annotation pipelines, showing that it provides a simple and effective means for converting genome sequences into community-accessible genome databases, particularly useful for emerging model organism projects with limited bioinformatics resources.The paper introduces MAKER, a portable and easily configurable genome annotation pipeline designed to facilitate the annotation of eukaryotic genomes and the creation of genome databases. MAKER identifies repeats, aligns ESTs and proteins to the genome, produces ab initio gene predictions, and integrates these data into gene annotations with evidence-based quality indices. The pipeline is highly customizable and trainable, allowing for the improvement of gene models through retraining. MAKER's outputs are compatible with the Generic Model Organism Database (GMOD) format, enabling direct integration into GMOD browsers and databases. The authors demonstrate MAKER's effectiveness by annotating the genome of the planarian *Schmidtea mediterranea* and creating a new genome database, SmedGD. They also compare MAKER's performance with other annotation pipelines, showing that it provides a simple and effective means for converting genome sequences into community-accessible genome databases, particularly useful for emerging model organism projects with limited bioinformatics resources.