Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset.
<p>The figure demonstrates six panels for different bootstrap thresholds (indicated in gray in the top bars). Boxes in panels indicate the central 50% (top and bottom of boxes) and the median (thicker black line in boxes) of the proportion of clusters recovered (Y axes) for a given set of pol-...
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2025
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| _version_ | 1849927626335977472 |
|---|---|
| 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 | 2025-11-25T18:41:38Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pcbi.1013676.g010 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Proportion_of_clusters_recovered_between_different_mixtures_of_pol_and_wgs_sequences_and_all_wgs_based_on_overlap_coefficient_full_dataset_/30714970 |
| 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 | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>The figure demonstrates six panels for different bootstrap thresholds (indicated in gray in the top bars). Boxes in panels indicate the central 50% (top and bottom of boxes) and the median (thicker black line in boxes) of the proportion of clusters recovered (Y axes) for a given set of pol-wgs mixture datasets (X axes). Whiskers indicate the range, and dots indicate outliers. Colors indicate overlap coefficient threshold to consider a cluster recovered. Higher values on the Y-axis indicate higher congruency in cluster inference between the mixture dataset and the wgs100 tree at the given bootstrap threshold.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_3beeb1400497ab9543a922abad5050a6 |
| identifier_str_mv | 10.1371/journal.pcbi.1013676.g010 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30714970 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset.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 demonstrates six panels for different bootstrap thresholds (indicated in gray in the top bars). Boxes in panels indicate the central 50% (top and bottom of boxes) and the median (thicker black line in boxes) of the proportion of clusters recovered (Y axes) for a given set of pol-wgs mixture datasets (X axes). Whiskers indicate the range, and dots indicate outliers. Colors indicate overlap coefficient threshold to consider a cluster recovered. Higher values on the Y-axis indicate higher congruency in cluster inference between the mixture dataset and the wgs100 tree at the given bootstrap threshold.</p>2025-11-25T18:41:38ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pcbi.1013676.g010https://figshare.com/articles/figure/Proportion_of_clusters_recovered_between_different_mixtures_of_pol_and_wgs_sequences_and_all_wgs_based_on_overlap_coefficient_full_dataset_/30714970CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/307149702025-11-25T18:41:38Z |
| spellingShingle | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. 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 | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. |
| title_full | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. |
| title_fullStr | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. |
| title_full_unstemmed | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. |
| title_short | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. |
| title_sort | Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. |
| 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 |