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chevron_left Protein-coding gene prediction Annotation workflows Genome annotation Pseudogene prediction ncRNA identification chevron_right

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MAKER-P specifications


Unique identifier OMICS_04638
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
License Artistic License version 2.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Mark Yandell

Publication for MAKER-P

MAKER-P citations


Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] mapped back to the assemblies (si appendix, table s4), and 94–98% of cegma () and busco () genes were detected (si appendix, table s5)., repetitive elements were identified following the standard maker-p recipe (, accessed october 2015) as described on the gmod site: (i) repeatmodeler with repeatscout v1.0.5, […]


Single molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome scale contiguity

PMCID: 5801600
PMID: 29253147
DOI: 10.1093/gigascience/gix124

[…] volume of transcript and protein sequence information generated from various experimental studies, the task of improving genome annotation of such genomes remains a major challenge. using the maker-p annotation pipeline (maker, rrid:scr_005309) [], publicly available transcriptome data of f. vesca, and protein sequences from arabidopsis thaliana and the uniprotkb database as evidence, […]


Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach

Front Genet
PMCID: 5723288
PMID: 29259619
DOI: 10.3389/fgene.2017.00180

[…] of satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of clementine, pummelo, and sweet orange. gene prediction by modeling with maker-p proposed 29,024 genes and 37,970 mrna; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. […]


Panax ginseng genome examination for ginsenoside biosynthesis

PMCID: 5710592
PMID: 29048480
DOI: 10.1093/gigascience/gix093

[…] against the te protein database. the tandem repeats in the genome assembly were identified through the tandem repeat finder., the gene models of the p. ginseng genome were predicted using the maker-p pipeline []. the available ginseng est, mrna datasets, and protein datasets were used to generate the first-pass gene annotation. the resulting gff3 file was used for ab initio gene predictor […]


Evidence based gene models for structural and functional annotations of the oil palm genome

Biol Direct
PMCID: 5591544
PMID: 28886750
DOI: 10.1186/s13062-017-0191-4

[…] using mega6 [] and mafft []. all programs were used with their default settings., a variety of tools has been developed for prediction and annotation of protein-coding genes, such as fgenesh++ [], maker-p [], gramene [], genemark [, ], and ensembl []. plant genomes (such as a. thaliana, medicago truncatula, o. sativa, e. guineensis, fragaria vesca and others) are generally annotated using […]


Draft Genome Sequence of the Phytopathogenic Fungus Fusarium euwallaceae, the Causal Agent of Fusarium Dieback

Genome Announc
PMCID: 5578843
PMID: 28860245
DOI: 10.1128/genomeA.00881-17

[…] trained for f. euwallaceae using webaugustus () and full coding sequences derived from a previously assembled transcriptome (unpublished data). augustus gene models were improved/corrected using the maker-p pipeline () and a database containing all of the proteins from the genomes of f. fujikuroi, f. graminearum, f. oxysporum, f. verticillioides, and f. solani (latest versions downloaded […]

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MAKER-P institution(s)
Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah

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