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PRANK specifications

Information


Unique identifier OMICS_12425
Name PRANK
Alternative name webPRANK
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format Fasta
Output format Fasta
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Ari Löytynoja <>
  • person_outline webPRANK <>

Additional information


A web interface is available at: https://www.ebi.ac.uk/goldman-srv/webprank/

Information


Unique identifier OMICS_12425
Name PRANK
Alternative name webPRANK
Interface Web user interface
Restrictions to use None
Input data DNA sequences, protein sequences.
Input format FASTA
Programming languages C++
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Ari Löytynoja <>
  • person_outline webPRANK <>

Additional information


A web interface is available at: https://www.ebi.ac.uk/goldman-srv/webprank/

Publications for PRANK

PRANK in pipelines

 (4)
2016
PMCID: 4750946
PMID: 26867150
DOI: 10.1371/journal.pntd.0004446

[…] were merged and paralogs were split by inspecting the conserved gene neighborhood around each sequence (5 genes on either side). each sequence for each cluster was independently aligned using prank [] (version 0.140603) and combined to form a multi-fasta alignment of the core genes., to facilitate the analysis of invasion assays, s. typhimurium sl1344 and s. weltevreden c2346, 10259, […]

2016
PMCID: 4792531
PMID: 26980512
DOI: 10.1093/database/bav127

[…] using infernal, and several trees are built using different substitution models. in parallel, a genomic alignment that includes the ncrna genes and their flanking sequence regions is built with prank. this alignment is used to create two additional phylogenetic trees using the neighbour-joining (nj) and maximum-likelihood (ml) methods. the trees arising from both the ncrna and genomic […]

2016
PMCID: 4958920
PMID: 27452401
DOI: 10.1038/srep30042

[…] of both clpp and accd we used all species of ericaceae where they are intact, i.e. uniflora, hypopitys, vaccinium and pyrola for clpp, and uniflora, hypopitys, arbutus and pyrola for accd. we chose prank for alignments of clpp and accd because it has been noted that for highly divergent sequences, dn/ds analysis performed on alignments generated by prank provides more precise results […]

2016
PMCID: 4980104
PMID: 27532052
DOI: 10.1126/sciadv.1600633

[…] be 2% greater than its second bit score., unaligned orthologous amino acid longest isoforms from galeopterus, tupaia, and cynocephalus were aligned to the existing raw amino acid alignment using prank (). any stop codon characters (“*” or “_”) were masked with “x” before alignment. this ensured proper reverse translation of amino acid alignments to amino acid–guided nucleotide alignments. […]


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PRANK in publications

 (50)
PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] sequences of each subunit were separately aligned with 14 different methods: l-ins-i, e-ins-i and g-ins-i strategies of mafft v7; psi-coffee, expresso; t-coffee; probcons v1.12; probalign v1.3; prank; muscle v3.7; msaprobs v0.9.7; kalign; dialign-tx; and clustal omega. the 10 best alignments were selected after evaluation with mumsa based on multiple overlap (mos) and average overlap (aos) […]

PMCID: 5924527
PMID: 29597328
DOI: 10.3390/genes9040185

[…] tree was drawn with figtree software []., the evolutionary history of apollo gene was inferred by using the maximum likelihood method. initial alignment of corresponding cds was performed using prank v.140110 [] in codon-aware mode. the alignment result was further used for building phylogenetic tree basing on the tamura-nei model [,]. the tree with the highest log likelihood (−12,153.79) […]

PMCID: 5808193
PMID: 29467729
DOI: 10.3389/fmicb.2018.00086

[…] manufacturer's instructions and sequenced at macrogen/south korea. all the sequences were aligned together with reference sequences (ncbi accession numbers ay560611, dq479323, and ay560612) using prank online (embl-ebi) (http://www.ebi.ac.uk/goldman-srv/webprank/) (löytynoja and goldman, ). a search for homing endonuclease genes (heg) was carried out for each sequenced intron using […]

PMCID: 5717227
PMID: 29208990
DOI: 10.1038/s41598-017-17051-4

[…] groups only contained one sequence from each of all species, this gene cluster was extracted as putative one-to-one orthologous. moreover, the cdss of the predicted orthologous genes were aligned by prank with “-f -codon” parameter. aligned sequences with ambiguous alignments were removed in further analysis. a manual check was also conducted to correct potential errors., to identify fegs […]

PMCID: 5664825
PMID: 29089032
DOI: 10.1186/s13059-017-1341-9

[…] classify the gene family. we assumed that the genes in the same clusters were in the same family and performed all-by-all alignments of the coding sequences within the clusters in each species using prank []. for each alignment result, the ks values were calculated using kaks calculator [] and single-linkage clustering for the ks values was performed using the hclust function in the r package. […]


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PRANK institution(s)
Institute of Biotechnology, University of Helsinki, Helsinki, Finland

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