Rates of different base frequencies from different mixture datasets.
<p>The figure explores the impact of the 4 different base frequency proportions (pi(A), pi(C), pi(G), pi(T), gray bar on top of each panel) in our choice of substitution model for IQTree (GTR+F+I+G4). Proportion is on the Y-axis, and the different mixture datasets are ordered from <i>pol...
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2025
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| _version_ | 1849927626361143296 |
|---|---|
| author | August Guang (9975678) |
| author2 | Casey W Dunn (21263816) Vlad Novitsky (3366560) Mark Howison (3315450) Rami Kantor (7863) |
| author2_role | author author author author |
| author_facet | August Guang (9975678) Casey W Dunn (21263816) Vlad Novitsky (3366560) Mark Howison (3315450) Rami Kantor (7863) |
| author_role | author |
| dc.creator.none.fl_str_mv | August Guang (9975678) Casey W Dunn (21263816) Vlad Novitsky (3366560) Mark Howison (3315450) Rami Kantor (7863) |
| dc.date.none.fl_str_mv | 2025-11-25T18:41:25Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pcbi.1013676.s003 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Rates_of_different_base_frequencies_from_different_mixture_datasets_/30714937 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Genetics Molecular Biology Biotechnology Evolutionary Biology Cancer Statistics Infectious Diseases Virology Biological Sciences not elsewhere classified still broadly used mean cluster size compared tree similarity also decreased number shape alignment provides flexible approach called larger clusters identified partial pol sequences 1 near full improve phylogenetic inference long hiv sequences phylogenetic inference near full 1 sequences shape alignments pol regions new approach molecular clusters improve phylogenetic full dataset short sequences long sequences available sequences xlink "> transmission dynamics systematically masked subset dataset study subset straightforward method short hiv shaped alignments results suggest provide insights proportional increments missing characters immediately depending different lengths analysis goals |
| dc.title.none.fl_str_mv | Rates of different base frequencies from different mixture datasets. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>The figure explores the impact of the 4 different base frequency proportions (pi(A), pi(C), pi(G), pi(T), gray bar on top of each panel) in our choice of substitution model for IQTree (GTR+F+I+G4). Proportion is on the Y-axis, and the different mixture datasets are ordered from <i>pol</i> to wgs100 on the X axis. Boxes in panels indicate the central 50% (top and bottom of boxes) and the median (thicker black line in boxes) of the proportions, whiskers indicate the range, and dots indicate outliers. There is a monotonic relationship between relative rate values and wgs proportion beginning with wgs10, when wgs sequences are introduced.</p> <p>(TIFF)</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_19ae83f994a4f9da76d76cb8e76afd8a |
| identifier_str_mv | 10.1371/journal.pcbi.1013676.s003 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30714937 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Rates of different base frequencies from different mixture datasets.August Guang (9975678)Casey W Dunn (21263816)Vlad Novitsky (3366560)Mark Howison (3315450)Rami Kantor (7863)GeneticsMolecular BiologyBiotechnologyEvolutionary BiologyCancerStatisticsInfectious DiseasesVirologyBiological Sciences not elsewhere classifiedstill broadly usedmean cluster sizecompared tree similarityalso decreased numbershape alignment providesflexible approach calledlarger clusters identifiedpartial pol sequences1 near fullimprove phylogenetic inferencelong hiv sequencesphylogenetic inferencenear full1 sequencesshape alignmentspol regionsnew approachmolecular clustersimprove phylogeneticfull datasetshort sequenceslong sequencesavailable sequencesxlink ">transmission dynamicssystematically maskedsubset datasetstudy subsetstraightforward methodshort hivshaped alignmentsresults suggestprovide insightsproportional incrementsmissing charactersimmediately dependingdifferent lengthsanalysis goals<p>The figure explores the impact of the 4 different base frequency proportions (pi(A), pi(C), pi(G), pi(T), gray bar on top of each panel) in our choice of substitution model for IQTree (GTR+F+I+G4). Proportion is on the Y-axis, and the different mixture datasets are ordered from <i>pol</i> to wgs100 on the X axis. Boxes in panels indicate the central 50% (top and bottom of boxes) and the median (thicker black line in boxes) of the proportions, whiskers indicate the range, and dots indicate outliers. There is a monotonic relationship between relative rate values and wgs proportion beginning with wgs10, when wgs sequences are introduced.</p> <p>(TIFF)</p>2025-11-25T18:41:25ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pcbi.1013676.s003https://figshare.com/articles/figure/Rates_of_different_base_frequencies_from_different_mixture_datasets_/30714937CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/307149372025-11-25T18:41:25Z |
| spellingShingle | Rates of different base frequencies from different mixture datasets. August Guang (9975678) Genetics Molecular Biology Biotechnology Evolutionary Biology Cancer Statistics Infectious Diseases Virology Biological Sciences not elsewhere classified still broadly used mean cluster size compared tree similarity also decreased number shape alignment provides flexible approach called larger clusters identified partial pol sequences 1 near full improve phylogenetic inference long hiv sequences phylogenetic inference near full 1 sequences shape alignments pol regions new approach molecular clusters improve phylogenetic full dataset short sequences long sequences available sequences xlink "> transmission dynamics systematically masked subset dataset study subset straightforward method short hiv shaped alignments results suggest provide insights proportional increments missing characters immediately depending different lengths analysis goals |
| status_str | publishedVersion |
| title | Rates of different base frequencies from different mixture datasets. |
| title_full | Rates of different base frequencies from different mixture datasets. |
| title_fullStr | Rates of different base frequencies from different mixture datasets. |
| title_full_unstemmed | Rates of different base frequencies from different mixture datasets. |
| title_short | Rates of different base frequencies from different mixture datasets. |
| title_sort | Rates of different base frequencies from different mixture datasets. |
| topic | Genetics Molecular Biology Biotechnology Evolutionary Biology Cancer Statistics Infectious Diseases Virology Biological Sciences not elsewhere classified still broadly used mean cluster size compared tree similarity also decreased number shape alignment provides flexible approach called larger clusters identified partial pol sequences 1 near full improve phylogenetic inference long hiv sequences phylogenetic inference near full 1 sequences shape alignments pol regions new approach molecular clusters improve phylogenetic full dataset short sequences long sequences available sequences xlink "> transmission dynamics systematically masked subset dataset study subset straightforward method short hiv shaped alignments results suggest provide insights proportional increments missing characters immediately depending different lengths analysis goals |