MAKER - The Genome Annotation Pipeline

MAKER is a portable and easy to configure genome annotation pipeline. It's purpose is to allow eukaryotic genome projects and prokaryotic genome projects to annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal. It outputs are in GFF3 and FASTA format, and can be directly loaded into Chado, GBrowse, JBrowse or Apollo.