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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
call_split See protocol

[…] 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, […]


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

[…] ason for such significant discrepancy was not clear, but repeat element that accounts for about 40% of the genome (Table ) may interfere with size estimation.The number of predicted genes and mRNA by MAKER-P (Campbell et al., ) were slightly higher than those of Clementine (Wu et al., ) but close to those of pummelo (Wang et al., ). Functional annotations identified the genes for each clan of the […]


Expert risk perceptions and the social amplification of risk: A case study in invasive tree pests and diseases

PMCID: 5637881
PMID: 29104513
DOI: 10.1016/j.envsci.2017.08.020

[…] y a Public Health England (PHE) systematic review of European literature, which concluded that OPM is a low risk to human health (O’Connell et al., 2015). In terms of PHE’s risk perceptions, a policy maker (P5) put this into context by indicating the need to balance the risks of OPM with other diseases: “We deal with meningitis and tuberculosis, where death and serious illness and significant publ […]


Panax ginseng genome examination for ginsenoside biosynthesis

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

[…] WuBlastX 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

[…] 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 a com […]


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 from the […]


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

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