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Citations per year

Number of citations per year for the bioinformatics software tool Staden

Tool usage distribution map

This map represents all the scientific publications referring to Staden per scientific context
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Staden specifications


Unique identifier OMICS_00894
Name Staden
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License BSD 2-clause “Simplified” License
Computer skills Medium
Stability Stable
Maintained Yes


  • Gap4
  • spin


No version available


  • person_outline James Bonfield

Publications for Staden

Staden citations


The first mitochondrial genomes for Pyralinae (Pyralidae) and Glaphyriinae (Crambidae), with phylogenetic implications of Pyraloidea

PLoS One
PMCID: 5870975
PMID: 29584761
DOI: 10.1371/journal.pone.0194672
call_split See protocol

[…] Contiguous sequences were assembled using Staden Package v1.7.0 []. PCGs and rRNA genes were identified based on homologous regions of published Pyraloidea mitogenomes using the Clustal X in MEGA 5 []. The tRNAscan-SE [] was used to predict t […]


Occurrence of Hepatozoon canis (Adeleorina: Hepatozoidae) and Anaplasma spp. (Rickettsiales: Anaplasmataceae) in black backed jackals (Canis mesomelas) in South Africa

PMCID: 5859442
PMID: 29554933
DOI: 10.1186/s13071-018-2714-y
call_split See protocol

[…] e High Pure Plasmid Isolation Kit (Roche Diagnostics, Mannheim, Germany). Sequencing was performed at InqabaBiotec™ (Pretoria, South Africa).The obtained sequences were assembled and edited using the GAP4 program of the Staden package (version 1.6.0 for Windows) []. A BLASTn homology search [] of GenBank was done using the full length consensus sequences. These were then aligned with 16S rRNA gene […]


Complete Genome Sequences of pLMA1 and pLMA7, Two Large Linear Plasmids of Micrococcus Strains Isolated from a High Altitude Lake in Argentina

Genome Announc
PMCID: 5823993
PMID: 29472322
DOI: 10.1128/genomeA.00010-18

[…] ds were end sequenced with an ABI 3730xl DNA sequencer (Life Technologies, Darmstadt, Germany), processed with Phred, and assembled using Phrap ( Sequence editing was done using GAP4 as part of the Staden software package (), and final gap closure was performed by PCR and primer walking using a Bio-X-Act kit (Bioline, London, United Kingdom).The linear plasmid pLMA1 was seque […]


Equid herpesvirus 8: Complete genome sequence and association with abortion in mares

PLoS One
PMCID: 5802896
PMID: 29414990
DOI: 10.1371/journal.pone.0192301

[…] An alignment containing the four Irish EHV-8 genome sequences and that of EHV-8 strain Wh was created by using Gap4 [], and used as the basis for comparison. Multiple sequence alignments of the predicted amino acid sequences of individual EHV-8 genes and of related genomes () were created by using Clustal impl […]


Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum

PMCID: 5852556
PMID: 29364862
DOI: 10.3390/genes9020060

[…] confirm the PacBio assemblies. The sequence of the smallest plasmid was assembled with MIRA v4.0.2 [] using both PacBio and Illumina reads. Contigs were ordered and joined using Abacas v1.3.1 [] and GAP4 [] included in the Staden package []. Finally, Circlator v1.0.0 [] was used to circularize sequences, to fix the origin of replication (dnaA in the chromosome and repA in plasmids), and to genera […]


Two new genera of metalmark butterflies of North and Central America (Lepidoptera, Riodinidae)

PMCID: 5799793
PMID: 29416392
DOI: 10.3897/zookeys.729.20179
call_split See protocol

[…] sion 3.1 cycle sequencing kit (Applied Biosystems, Inc.) and an ABI 3100 automated DNA sequencer (Applied Biosystems, Inc.) using the amplification primers. Sequences were assembled and edited in the STADEN PACKAGE version 1.6.0 (). […]

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Staden institution(s)
Laboratory of Molecular Biology, Hills Road, CB, Cambridge, UK

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