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MAKER is a portable and easy to configure genome annotation pipeline. It's purpose is to allow smaller eukaryotic 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 or FASTA format, and can be directly loaded into Chado, GBrowse, and Apollo.

Note that MAKER is designed for eukaryotic genomes. If you wish to annotate prokaryotic genomes please contact the Yandell lab for other options.


The MAKER genome annotation pipeline generates several different types of annotations, including
  • ab-initio gene predictions from both SNAP and MAKER
  • EST alignments from both EXONERATE and BLASTN
  • Protein alignments from EXONERATE and BLASTX
  • Repeats
MAKER generated annotations, shown in Apollo.



MAKER, by default runs on a single computer. A parallel version, mpi_maker, is also available. To run mpi_maker you will need an MPI package installed on all participating computers. Try MPICH2. Remember to install MPICH2 with the --enable-sharedlibs flag set to the appropriate value (See theMPICH2 Installer's Guide.)


MAKER documentation is available from these sources:

Read both the paper and the README before installing MAKER.


A compressed TAR file is available at


MAKER comes with sample data for testing purposes. See the /data directory in the download.

Since MAKER is a command driven pipeline there are no screenshots or online demos available.

Mailing List

MAKER is maintained by the Mark Yandell Lab at the University of Utah. There is not yet a mailing list.


Mark Yandell <>