PAGAN protocols

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PAGAN specifications

Information


Unique identifier OMICS_11525
Name PAGAN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ari Löytynoja <>

Publication for PAGAN

PAGAN in pipeline

2017
PMCID: 5736351
PMID: 29256859
DOI: 10.7554/eLife.30637.066

[…] mrsa252, that is reference panel iv. this allowed us to distinguish orthologs from paralogs in the next step in which we multiply aligned all coding sequences overlapping those in mrsa252 using pagan (). after removing sequences with premature stop codons, we analyzed each alignment of between two and 16 genes using a modification of omegamap (), assuming all sites were unlinked. […]


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PAGAN in publications

 (7)
PMCID: 5736351
PMID: 29256859
DOI: 10.7554/eLife.30637.066

[…] mrsa252, that is reference panel iv. this allowed us to distinguish orthologs from paralogs in the next step in which we multiply aligned all coding sequences overlapping those in mrsa252 using pagan (). after removing sequences with premature stop codons, we analyzed each alignment of between two and 16 genes using a modification of omegamap (), assuming all sites were unlinked. […]

PMCID: 5123300
DOI: 10.1186/s12864-016-3101-8

[…] msa method, this extension can be easily done. thus, methods such as statalign [], which may be limited to even smaller datasets, could also be tested in this framework. similarly, methods such as pagan [] are impacted by dataset size and the challenge in estimating good guide trees, and pasta’s phylogenetically-informed divide-and-conquer strategy might be useful techniques to improve […]

PMCID: 5010716
PMID: 27590526
DOI: 10.1186/s12862-016-0743-8

[…] tools are extremely sensitive to alignment errors, when aligning p53 codon sequences, we manually inspected, using aliview alignment editor [], the results of two codon-alignment methods: (1) pagan v.0.47 [] and (2) the method implemented by the selecton server [], which is based on muscle multiple alignment []. due to an ambiguous result for amino acid residues in the disordered tad2 […]

PMCID: 5008119
PMID: 27584086
DOI: 10.1038/srep32372

[…] to include in a full-family phylogenetic analysis due to high sequence diversity. to obtain a reliable lipocalin alignment (as defined using guidance), three alignments were produced using the pagan, mafft, and clustalw algorithms. for a sequence-based phylogeny of lipocalins, the three amino acid sequence alignments (see materials and methods) were used to build nj, ml and mp phylogenetic […]

PMCID: 4287568
PMID: 25282640
DOI: 10.1186/1471-2105-15-338

[…] omega v1.1.0 [] (default)◦ mafft fft-ns-i v7.029b []–anysymbol –retree 1 –maxiterate 0 –unweight◦ mafft l-ins-i v7.029b []–anysymbol –retree 1 –maxiterate 0 –unweight◦ muscle v3.8.31 [] -maxiters 1◦ pagan v.0.47 [] (default), ◦ clustal omega v1.1.0 [] (default), ◦ mafft fft-ns-i v7.029b [], –anysymbol –retree 1 –maxiterate 0 –unweight, ◦ mafft l-ins-i v7.029b [], –anysymbol –retree 1 –maxiterate […]


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PAGAN institution(s)
EMBL-European Bioinformatics Institute, Hinxton, UK; Institute of Biotechnology, University of Helsinki, Finland
PAGAN funding source(s)
Wellcome Trust [GR078968]; Biocenter Finland

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