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Protocols

GenomeTools specifications

Information


Unique identifier OMICS_16119
Name GenomeTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BED, .GFF, .GTF, .GVF
Output format BED, .GFF, .GTF, .GVF
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Python, Ruby
License Other
Computer skills Advanced
Stability Stable
Requirements
Cygwin
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Stefan Kurtz

Publication for GenomeTools

GenomeTools citations

 (31)
call_split

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

2018
Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115
call_split See protocol

[…] sed October 2015) as described on the GMOD site: (i) RepeatModeler with Repeatscout v1.0.5, Recon v1.08, RepeatMasker version open4.0.5, using RepBase version 20140131 () and TandemRepeatFinder; (ii) GenomeTools LTRharvest and LTRdigest (); (iii) MITEhunter with default parameters (). We generated species-specific repeat libraries for P. andersonii and T. orientalis separately and combined these i […]

library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] extension penalty 1, Z-best 10. Alignments were viewed in IGV [], Tablet version 1.16.09.06 [] and SAMtools Tview version 0.1.19-96b5f2294a [].Genome nucleotide pairwise distance was calculated with GenomeTools version 1.5.8 genomediff []. Andi [], with Kimura modelling and anchor pair significance of 0.05 was also used for calculating genomic distances and 1000-time bootstrap. Whole genome phylo […]

library_books

Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

2018
Front Genet
PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] e (). The pipeline is available at http://doi.org/10.5281/zenodo.1098651.Long terminal repeat (LTR) elements were detected using two parallel runs of the LTR harvest () and LTRdigest () packages from Genometools v1.5.8 (). Recent insertions of LTR elements were detected by setting the similarity cutoff in LTR harvest to 99% and only including repeats with a TGCA palindromic motif sequence. The LTR […]

library_books

Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

2018
BMC Genomics
PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] A library of repeated elements was created as described in []. RepeatModeler v1.0.8, LTRharvest [] part of genometools v1.5.7 and TransposonPSI were used in combination to create a set of putative repeats. Elements with only a match against an UniProtKB/SwissProt database and not against the database of kn […]

library_books

A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination

2018
PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] qiagenbioinformatics.com/) with Kimura substitution model and 2000 bootstrap replicates. The phylogenetic tree image was generated using iTOL version 3 (). Gene model tracks (; ) were generated using GenomeTools (). […]

library_books

Improving the annotation of the Heterorhabditis bacteriophora genome

2018
GigaScience
PMCID: 5906903
PMID: 29617768
DOI: 10.1093/gigascience/giy034

[…] d from the protein FASTA files. The GFF file for the published gene predictions did not contain any isoforms and was analyzed in its entirety. f Introns were inferred for the published GFF file using GenomeTools v1.5.9 in -addintrons mode []. Intron frequencies were then calculated for the published and BRAKER1 annotations from their respective GFF files. Exon frequencies were calculated for the p […]

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GenomeTools institution(s)
Center for Bioinformatics, University of Hamburg, Hamburg, Germany

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