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Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-23747
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dc.contributor.authorMaiolo, Massimo-
dc.contributor.authorGatti, Lorenzo-
dc.contributor.authorFrei, Diego-
dc.contributor.authorLeidi, Tiziano-
dc.contributor.authorGil, Manuel-
dc.contributor.authorAnisimova, Maria-
dc.date.accessioned2021-12-11T13:37:56Z-
dc.date.available2021-12-11T13:37:56Z-
dc.date.issued2021-10-24-
dc.identifier.issn1471-2105de_CH
dc.identifier.urihttps://digitalcollection.zhaw.ch/handle/11475/23747-
dc.description.abstractBackground Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the phylogeny relating the input sequences. Results We present a new progressive multiple sequence alignment tool ProPIP. The process of insertions and deletions is described using an explicit evolutionary model—the Poisson Indel Process or PIP. The method is based on dynamic programming and is implemented in a frequentist framework. The source code can be compiled on Linux, macOS and Microsoft Windows platforms. The algorithm is implemented in C++ as standalone program. The source code is freely available on GitHub at https://github.com/acg-team/ProPIP and is distributed under the terms of the GNU GPL v3 license. Conclusions The use of an explicit indel evolution model allows to avoid over-alignment, to infer gaps in a phylogenetically consistent way and to make inferences about the rates of insertions and deletions. Instead of the arbitrary gap penalties, the parameters used by ProPIP are the insertion and deletion rates, which have biological interpretation and are contextualized in a probabilistic environment. As a result, indel rate settings may be optimised in order to infer phylogenetically meaningful gap patterns.de_CH
dc.language.isoende_CH
dc.publisherBioMed Centralde_CH
dc.relation.ispartofBMC Bioinformaticsde_CH
dc.rightshttp://creativecommons.org/licenses/by/4.0/de_CH
dc.subjectAlignment softwarede_CH
dc.subjectDynamic programmingde_CH
dc.subjectEvolutionary alignmentde_CH
dc.subjectIndel evolutionde_CH
dc.subjectMultiple sequence alignmnetde_CH
dc.subjectPoisson Indel Processde_CH
dc.subjectAlgorithmde_CH
dc.subjectPhylogenyde_CH
dc.subjectSequence alignmentde_CH
dc.subjectSoftwarede_CH
dc.subjectEvolution, molecularde_CH
dc.subjectINDEL mutationde_CH
dc.subject.ddc005: Computerprogrammierung, Programme und Datende_CH
dc.titleProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Processde_CH
dc.typeBeitrag in wissenschaftlicher Zeitschriftde_CH
dcterms.typeTextde_CH
zhaw.departementLife Sciences und Facility Managementde_CH
zhaw.organisationalunitInstitut für Computational Life Sciences (ICLS)de_CH
dc.identifier.doi10.1186/s12859-021-04442-8de_CH
dc.identifier.doi10.21256/zhaw-23747-
dc.identifier.pmid34689750de_CH
zhaw.funding.euNode_CH
zhaw.issue1de_CH
zhaw.originated.zhawYesde_CH
zhaw.pages.start518de_CH
zhaw.publication.statuspublishedVersionde_CH
zhaw.volume22de_CH
zhaw.publication.reviewPeer review (Publikation)de_CH
zhaw.funding.snf157064, 176316de_CH
zhaw.webfeedBiomedical String Analysisde_CH
zhaw.webfeedComputational Genomicsde_CH
zhaw.funding.zhawFast joint estimation of alignment and phylogeny from genomics sequences in a frequentist frameworkde_CH
zhaw.author.additionalNode_CH
zhaw.display.portraitYesde_CH
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Maiolo, M., Gatti, L., Frei, D., Leidi, T., Gil, M., & Anisimova, M. (2021). ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics, 22(1), 518. https://doi.org/10.1186/s12859-021-04442-8
Maiolo, M. et al. (2021) ‘ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process’, BMC Bioinformatics, 22(1), p. 518. Available at: https://doi.org/10.1186/s12859-021-04442-8.
M. Maiolo, L. Gatti, D. Frei, T. Leidi, M. Gil, and M. Anisimova, “ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process,” BMC Bioinformatics, vol. 22, no. 1, p. 518, Oct. 2021, doi: 10.1186/s12859-021-04442-8.
MAIOLO, Massimo, Lorenzo GATTI, Diego FREI, Tiziano LEIDI, Manuel GIL und Maria ANISIMOVA, 2021. ProPIP : a tool for progressive multiple sequence alignment with Poisson Indel Process. BMC Bioinformatics. 24 Oktober 2021. Bd. 22, Nr. 1, S. 518. DOI 10.1186/s12859-021-04442-8
Maiolo, Massimo, Lorenzo Gatti, Diego Frei, Tiziano Leidi, Manuel Gil, and Maria Anisimova. 2021. “ProPIP : A Tool for Progressive Multiple Sequence Alignment with Poisson Indel Process.” BMC Bioinformatics 22 (1): 518. https://doi.org/10.1186/s12859-021-04442-8.
Maiolo, Massimo, et al. “ProPIP : A Tool for Progressive Multiple Sequence Alignment with Poisson Indel Process.” BMC Bioinformatics, vol. 22, no. 1, Oct. 2021, p. 518, https://doi.org/10.1186/s12859-021-04442-8.


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