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PAGAN specifications


Unique identifier OMICS_11525
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




No version available



  • person_outline Ari Löytynoja

Publication for PAGAN

PAGAN citations


Severe infections emerge from commensal bacteria by adaptive evolution

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

[…] ainst 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. We previous […]


Scaling statistical multiple sequence alignment to large datasets

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

[…] se 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 their sc […]


Adaptive patterns in the p53 protein sequence of the hypoxia and cancer tolerant blind mole rat Spalax

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

[…] nalysis 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 when […]


Substrate prediction of Ixodes ricinus salivary lipocalins differentially expressed during Borrelia afzelii infection

Sci Rep
PMCID: 5008119
PMID: 27584086
DOI: 10.1038/srep32372

[…] ficult 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 […]


Systematic exploration of guide tree topology effects for small protein alignments

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

[…] rs construct an initial alignment, without iteration. We call this alignment the default-tree alignment as it uses the default guide-tree, despite not using default command-line flags. The version of PAGAN that we used does not construct a default guide-tree. In a next step we use the ML tree as the guide-tree, again without iteration. We then used all possible guide-trees to align the sequences. […]


A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data

PMCID: 4096371
PMID: 24793089
DOI: 10.1534/genetics.114.161299

[…] examples also give some guidance for appropriate applications of the model.If reference trees are available, researchers may use phylogeny-aware alignment algorithms such as pplacer, EPA, PaPaRa, or PAGAN (; ; ; ). Although the approach varies, each of these methods aligns read data to guide alignments using reference trees to determine the best homology. The read-placement counts on the tree cou […]


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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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