PRANK pipeline

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)
2017
PMCID: 5293829
PMID: 28223970
DOI: 10.3389/fmicb.2017.00156

[…] 20mers at each base, we were able to (1) map recombinant boundaries and (2) ascertain the extent of mixed populations using r software (r development core team, 2015)., genes were aligned using prank (löytynoja, 2014). the r package phangorn (schliep, 2010) was used to calculate maximum likelihood phylogeny using the symmetric+gi model (chosen based on best fit). trees were bootstrapped 100 […]

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 (40). 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. […]

2015
PMCID: 4678570
PMID: 26667623
DOI: 10.1186/s12862-015-0554-3

[…] (unpublished observation). further tests consistently demonstrated very similar topologies for trees based on multiple sequence alignments prepared in webpranks [45] or muscle [46]. only the webprank-based results, that consistently had better statistical support, are shown here. the rooted tree based on 49 macit sequences and rendered from phylogenetic inference analysis […]

2012
PMCID: 3447340
PMID: 23015776
DOI: 10.3390/md10081812

[…] a phylogenetic tree of cytolysins using only actinoporins with evidence at transcript level and with full-length sequences. a multiple sequence alignment of amino acids with 533 sites, was made with webprank [31] followed by an analysis to choose the best fit model for protein evolution with prottest [31], that gave wag model. a maximum likelihood tree reconstruction was made in mega 5 [32] […]

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

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