MAKER is an easy-to-use genome annotation pipeline designed for emerging model organism genomes. It allows investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and synthesizes these data into gene annotations with evidence-based quality indices. It is easily trainable, using outputs of preliminary runs to retrain its gene-prediction algorithm for higher-quality gene models. MAKER's inputs are minimal, and its outputs can be used to create a GMOD database or viewed in the Apollo Genome browser. MAKER was used to annotate the genome of the planarian Schmidtea mediterranea and create a new genome database, SmedGD. It was also compared to other annotation pipelines, demonstrating its effectiveness in converting genome sequences into community-accessible databases. Genome annotation is becoming a bottleneck in genomics, with new genomes being sequenced faster than they are annotated. MAKER addresses this by providing a simple, portable, and configurable pipeline that can be used by researchers with limited bioinformatics experience. It is designed to be user-friendly, with outputs compatible with GMOD and Apollo, allowing annotation, viewing, and editing of individual contigs and BACs without a database. MAKER's performance was benchmarked on the C. elegans genome, showing it comparable to other pipelines in terms of accuracy and completeness. It was also tested on the S. mediterranea genome, where it produced high-quality annotations and a comprehensive gene set. MAKER's performance on S. mediterranea was particularly strong, with a higher enrichment of protein-domain containing annotations compared to C. elegans. It improved upon SNAP's ab initio predictions, especially in emerging genomes with limited training data. MAKER's outputs are compatible with GMOD and Apollo, enabling the creation of genome databases and facilitating data sharing. MAKER is ideal for small-scale projects and emerging model organisms, providing a first round of database-ready annotations. It is also modular, allowing integration of various gene predictors and future improvements such as ncRNA annotations. MAKER is publicly available, with source code and documentation provided for easy use and customization.MAKER is an easy-to-use genome annotation pipeline designed for emerging model organism genomes. It allows investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and synthesizes these data into gene annotations with evidence-based quality indices. It is easily trainable, using outputs of preliminary runs to retrain its gene-prediction algorithm for higher-quality gene models. MAKER's inputs are minimal, and its outputs can be used to create a GMOD database or viewed in the Apollo Genome browser. MAKER was used to annotate the genome of the planarian Schmidtea mediterranea and create a new genome database, SmedGD. It was also compared to other annotation pipelines, demonstrating its effectiveness in converting genome sequences into community-accessible databases. Genome annotation is becoming a bottleneck in genomics, with new genomes being sequenced faster than they are annotated. MAKER addresses this by providing a simple, portable, and configurable pipeline that can be used by researchers with limited bioinformatics experience. It is designed to be user-friendly, with outputs compatible with GMOD and Apollo, allowing annotation, viewing, and editing of individual contigs and BACs without a database. MAKER's performance was benchmarked on the C. elegans genome, showing it comparable to other pipelines in terms of accuracy and completeness. It was also tested on the S. mediterranea genome, where it produced high-quality annotations and a comprehensive gene set. MAKER's performance on S. mediterranea was particularly strong, with a higher enrichment of protein-domain containing annotations compared to C. elegans. It improved upon SNAP's ab initio predictions, especially in emerging genomes with limited training data. MAKER's outputs are compatible with GMOD and Apollo, enabling the creation of genome databases and facilitating data sharing. MAKER is ideal for small-scale projects and emerging model organisms, providing a first round of database-ready annotations. It is also modular, allowing integration of various gene predictors and future improvements such as ncRNA annotations. MAKER is publicly available, with source code and documentation provided for easy use and customization.