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dc.contributor.authorGrievink, Liat Shavit
dc.contributor.authorPenny, David
dc.contributor.authorHendy, Mike D
dc.contributor.authorHolland, Barbara R
dc.date.accessioned2010-10-07T03:27:57Z
dc.date.accessioned2016-03-06T22:26:00Z
dc.date.accessioned2016-09-07T13:57:44Z
dc.date.availableNO_RESTRICTIONen_US
dc.date.available2010-10-07T03:27:57Z
dc.date.available2016-03-06T22:26:00Z
dc.date.available2016-09-07T13:57:44Z
dc.date.issued2008-11-21
dc.identifier.citationGrievink, L. S., Penny, D., Hendy, M. D., & Holland, B. R. (2008). LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. Bmc Evolutionary Biology, 8(317). doi: 10.1186/1471-2148-8-317en_US
dc.identifier.issn1471-2148
dc.identifier.urihttp://hdl.handle.net/10179/9703
dc.description.abstractBackground: Commonly used phylogenetic models assume a homogeneous evolutionary process throughout the tree. It is known that these homogeneous models are often too simplistic, and that with time some properties of the evolutionary process can change (due to selection or drift). In particular, as constraints on sequences evolve, the proportion of variable sites can vary between lineages. This affects the ability of phylogenetic methods to correctly estimate phylogenetic trees, especially for long timescales. To date there is no phylogenetic model that allows for change in the proportion of variable sites, and the degree to which this affects phylogenetic reconstruction is unknown. Results: We present LineageSpecificSeqgen, an extension to the seq-gen program that allows generation of sequences with both changes in the proportion of variable sites and changes in the rate at which sites switch between being variable and invariable. In contrast to seq-gen and its derivatives to date, we interpret branch lengths as the mean number of substitutions per variable site, as opposed to the mean number of substitutions per site (which is averaged over all sites, including invariable sites). This allows specification of the substitution rates of variable sites, independently of the proportion of invariable sites. Conclusion: LineageSpecificSeqgen allows simulation of DNA and amino acid sequence alignments under a lineage-specific evolutionary process. The program can be used to test current models of evolution on sequences that have undergone lineage-specific evolution. It facilitates the development of both new methods to identify such processes in real data, and means to account for such processes. The program is available at: http://awcmee.massey.ac.nz/downloads.htm.en_US
dc.language.isoenen_US
dc.publisherBiomed Centralen_US
dc.relation.isformatofhttp://www.biomedcentral.com/1471-2148/8/317en_US
dc.relation.isbasedonBiomed Centralen_US
dc.rights2009 Grievink et al; licen see BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the orig inal work is properly cited.
dc.subjectSoftwareen_US
dc.subjectSimulationen_US
dc.subjectSeq-genen_US
dc.subject.otherFields of Research::280000 Information, Computing and Communication Sciences::280300 Computer Software::280302 Software engineeringen_US
dc.titleLineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sitesen_US
dc.typeJournal Articleen_US
dc.identifier.harvestedMassey_Dark
dc.identifier.harvestedMassey_Dark


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