An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
Publication Date
November 26, 2009
Journal
PLOS Computational Biology
Authors
Sergei L. Kosakovsky Pond, David Posada, Eric Stawiski, Colombe Chappey, et al
Volume
5
Issue
11
Pages
e1000581
DOI
http://doi.org/10.1371/journal.pcbi.1000581
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000581
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19956739
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776870
Europe PMC
http://europepmc.org/abstract/MED/19956739
Web of Science
000274228500029
Scopus
73449085165
Mendeley
http://www.mendeley.com/research/evolutionary-modelbased-algorithm-accurate-phylogenetic-breakpoint-mapping-subtype-prediction-hiv1
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Mendeley | Further Information

{"title"=>"An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1", "type"=>"journal", "authors"=>[{"first_name"=>"Sergei L Kosakovsky", "last_name"=>"Pond", "scopus_author_id"=>"7801633431"}, {"first_name"=>"David", "last_name"=>"Posada", "scopus_author_id"=>"6701851414"}, {"first_name"=>"Eric", "last_name"=>"Stawiski", "scopus_author_id"=>"6507625006"}, {"first_name"=>"Colombe", "last_name"=>"Chappey", "scopus_author_id"=>"24755080900"}, {"first_name"=>"Art F Y", "last_name"=>"Poon", "scopus_author_id"=>"15073114700"}, {"first_name"=>"Gareth", "last_name"=>"Hughes", "scopus_author_id"=>"7402326886"}, {"first_name"=>"Esther", "last_name"=>"Fearnhill", "scopus_author_id"=>"15848068800"}, {"first_name"=>"Mike B.", "last_name"=>"Gravenor", "scopus_author_id"=>"7004369951"}, {"first_name"=>"Andrew J Leigh", "last_name"=>"Brown", "scopus_author_id"=>"56901598900"}, {"first_name"=>"Simon D W", "last_name"=>"Frost", "scopus_author_id"=>"7102366418"}], "year"=>2009, "source"=>"PLoS Computational Biology", "identifiers"=>{"scopus"=>"2-s2.0-73449085165", "doi"=>"10.1371/journal.pcbi.1000581", "isbn"=>"1553-7358 (Electronic)\\n1553-734X (Linking)", "sgr"=>"73449085165", "issn"=>"1553734X", "pui"=>"358053161", "pmid"=>"19956739"}, "id"=>"31ab6ed5-7afb-3f0d-9e42-3fe4f2dd9e79", "abstract"=>"Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (approximately 5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate, robust and extensible subtyping procedures is clear.", "link"=>"http://www.mendeley.com/research/evolutionary-modelbased-algorithm-accurate-phylogenetic-breakpoint-mapping-subtype-prediction-hiv1", "reader_count"=>85, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>27, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>5, "Student > Master"=>10, "Other"=>1, "Student > Bachelor"=>10, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>27, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>5, "Student > Master"=>10, "Other"=>1, "Student > Bachelor"=>10, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_subject_area"=>{"Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Mathematics"=>2, "Medicine and Dentistry"=>12, "Agricultural and Biological Sciences"=>53, "Computer Science"=>10, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>53}, "Computer Science"=>{"Computer Science"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Netherlands"=>1, "Belgium"=>1, "United States"=>1, "Brazil"=>3, "Italy"=>1, "Spain"=>1}, "group_count"=>5}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/874330"], "description"=>"<p>The SCUEAL clustering plots present in this figure and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000581#pcbi-1000581-g007\" target=\"_blank\">Figures 7</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000581#pcbi-1000581-g008\" target=\"_blank\">8</a> and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000581#pcbi-1000581-g009\" target=\"_blank\">9</a> are conceptually analogous to bootscan plots, i.e. which reference sequence is the most likely sister lineage of the query sequence for a given site, but is based on model averaged support values instead of phylogenetic bootstrap. A partial reference tree with placed query is shown; color coding is consistent between the similarity plot and the tree. A phylogenetic tree with bootstrap support values and bootscan plot using the REGA alignment generated for the query sequence are shown.</p>", "links"=>[], "tags"=>["scueal", "rega", "classifying", "pol", "subtype"], "article_id"=>544768, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g006", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_of_a_good_agreement_between_SCUEAL_and_REGA_in_classifying_a_partial_pol_subtype_B_sequence_/544768", "title"=>"An example of a good agreement between SCUEAL and REGA in classifying a partial pol subtype B sequence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:19:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/873742"], "description"=>"<p>Algorithmic logic underlying SCUEAL; see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000581#pcbi-1000581-g003\" target=\"_blank\">Figure 3</a> for a description of the genetic algorithm itself. Refer to the text for more detailed descriptions of individual procedures and parameter definitions.</p>", "links"=>[], "tags"=>["flowchart"], "article_id"=>544192, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Algorithmic_flowchart_of_SCUEAL_/544192", "title"=>"Algorithmic flowchart of SCUEAL.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:09:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/874893"], "description"=>"<p><b>Subtype</b> lists the sequence subtype as annotated in the database. <b>Sequences</b> provides the number of sequences downloaded from the database. <b>Agree</b> gives the percentage of sequences for which SCUEAL returned the same subtype as that stored in the database. <b>within-subtype</b>–SCUEAL inferred within-subtype recombination within the same subtype as the one stored in the database; figures in parentheses show the proportion of within-subtype recombinants identified when DRAM positions were masked. <b>Diff. pure subtype</b>–the proportion of cases where SCUEAL inferred a pure subtype different from the annotated one. <b>Diff. recombinant</b>–the proportion of cases where SCUEAL inferred a recombinant mosaic with at least one fragment different from the annotated subtype; figures in parentheses show the proportion of within-subtype recombinants identified when DRAM positions were masked. <b>Top 3 CRFs and URFs</b>–three most frequent mosaics inferred by SCUEAL.</p>", "links"=>[], "tags"=>["hiv-1", "transcriptase", "sequences", "stanford"], "article_id"=>545342, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SCUEAL_screening_results_on_partial_HIV_1_reverse_transcriptase_sequences_from_the_Stanford_Drug_Resistance_database_/545342", "title"=>"SCUEAL screening results on partial HIV-1 reverse transcriptase sequences from the Stanford Drug Resistance database.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-26 01:29:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/874041"], "description"=>"<p>One of the simulation scenarios used to asses our detection method with the results over replicates (scenario 5/close in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000581#pcbi-1000581-t002\" target=\"_blank\">Table 2</a>). The query sequence (2) was simulated to move from reference lineage 1 to reference lineage 3 every 400 bp as shown in the tree panel. The clustering chart depicts model and replicate averaged support for assigning the query sequence to a particular reference lineage, as estimated by the genetic algorithm over 100 simulated data replicates, whereas black impulse plots indicate the inferred placements of breakpoints. The y-axis does not reach because each replicate contributes the model averaged support for the best inferred mosaic type–a value that is ; the upper limit on the y-axis is, therefore, the mean (over replicates) model-averaged support for the best-fitting mosaic (0.92 in this case).</p>", "links"=>[], "tags"=>["simulation"], "article_id"=>544492, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_simulation_scenario_example_/544492", "title"=>"A simulation scenario example.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:14:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/873615"], "description"=>"<p>Panel A: a phylogenetic breakpoint/lineage model which “threads” a query sequence (labeled ‘Q’) onto the reference tree with sequences. Panel B: the example individual model (mosaic) is encoded by a 36-bit binary vector on 5 fragments (genes)–2 for placing the breakpoints (Gray-binary encoded) and 3 for identifying sister lineages, binary encoded using the post-order traversal scheme shown in the reference tree of Panel A.</p>", "links"=>[], "tags"=>["concepts", "mosaic", "binary", "encoding", "algorithm"], "article_id"=>544058, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_to_illustrate_the_concepts_of_a_mosaic_and_its_binary_encoding_upon_which_the_genetic_algorithm_operates_/544058", "title"=>"An example to illustrate the concepts of a mosaic and its binary encoding upon which the genetic algorithm operates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:07:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/874587"], "description"=>"<p>An example of within-subtype (B) recombination detected by SCUEAL, but not by REGA. A partial reference tree with placed query is shown; color coding is consistent between the similarity plot and the tree.</p>", "links"=>[], "tags"=>["within-subtype", "recombination", "placed", "query", "coding"], "article_id"=>545031, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g008", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_of_within_subtype_B_recombination_detected_by_SCUEAL_but_not_by_REGA_A_partial_reference_tree_with_placed_query_is_shown_color_coding_is_consistent_between_the_similarity_plot_and_the_tree_/545031", "title"=>"An example of within-subtype (B) recombination detected by SCUEAL, but not by REGA. A partial reference tree with placed query is shown; color coding is consistent between the similarity plot and the tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:23:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/874931"], "description"=>"<p><b>Scenario provides a brief description a given simulation scenario. Seq., sites</b> lists the number and length of simulated sequences. <b>Type/distance</b> classifies the simulation scenario by type and mean divergence between parental strains, measured as the total branch length (expected number of substitutions/site 100%) between the strains. <b>Inferred Mosaics</b> tabulates the number of cases (and the number of those that matched or bested the BIC score of the correct model) that fell into each of the classification categories (see main text for further detail). Correct: the simulated mosaic was recovered; superset: the simulated mosaic and superfluous breakpoints were inferred; subset: a partial correct mosaic was recapitulated (some breakpoints missing); and M/M - the inferred mosaic was a mismatch with the generating one. <b>Breakpoints</b> enumerates the location of each simulated breakpoint and its parental lineages, the number of times the breakpoint was recovered by SCUEAL, and the median (2.5%–97.5% range) of the distribution of distances between the simulated and inferred breakpoints.</p>", "links"=>[], "tags"=>["simulated"], "article_id"=>545384, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.t001", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SCUEAL_performance_on_simulated_data_/545384", "title"=>"SCUEAL performance on simulated data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-26 01:29:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/874740"], "description"=>"<p>Similarity plots based on the reduced REGA alignments (only A and B subtype reference sequences) confirm that the same mosaic structure is supported using if a small enough window is selected for a sliding window analysis.</p>", "links"=>[], "tags"=>["assigned", "subtype", "rega", "deduced", "a-b-a", "mosaic"], "article_id"=>545190, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g009", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_instance_when_a_sequence_assigned_to_subtype_A_by_REGA_is_deduced_to_be_an_A_B_A_mosaic_by_SCUEAL_/545190", "title"=>"An instance when a sequence assigned to subtype A by REGA is deduced to be an A-B-A mosaic by SCUEAL.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:26:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/874159"], "description"=>"<p>Power of SCUEAL to detect breakpoints in the HIV-1 pol sequence shuffling scenario as a function of recombinant fragment length (x-axis) and divergence between parental strains (y-axis). Grid cells are colored according to the proportion of correctly detected breakpoints (different cells may summarize different numbers of simulations). White squares are plotted when there were no simulated breakpoints within a corresponding length-divergence range of values.</p>", "links"=>[], "tags"=>["shuffling"], "article_id"=>544611, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Power_and_accuracy_in_the_sequence_shuffling_simulation_/544611", "title"=>"Power and accuracy in the sequence shuffling simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:16:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/874849"], "description"=>"<p><b>Subtype</b> lists the sequence subtype as annotated in the database. <b>Sequences</b> provides the number of sequences downloaded from the database. <b>Agree</b> gives the percentage of sequences for which SCUEAL returned the same subtype as the one inferred by REGA. <b>within-subtype</b>–SCUEAL inferred within-subtype recombination within the same subtype as the one inferred by REGA; figures in parentheses show the proportion of within-subtype recombinants identified when DRAM positions were masked. <b>Diff. pure subtype</b>–the proportion of cases where SCUEAL inferred a pure subtype different from the REGA assignment. <b>Diff. recombinant</b>–the proportion of cases where SCUEAL inferred a recombinant mosaic with at least one fragment different from the annotated subtype; figures in parentheses show the proportion of within-subtype recombinants identified when DRAM positions were masked. <b>Top 3 CRFs and URFs</b>–three most frequent mosaics inferred by SCUEAL.</p>", "links"=>[], "tags"=>["hiv-1", "polymerase", "sequences"], "article_id"=>545295, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.t003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SCUEAL_screening_results_on_partial_HIV_1_polymerase_sequences_from_the_UK_/545295", "title"=>"SCUEAL screening results on partial HIV-1 polymerase sequences from the UK.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-26 01:28:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/873883"], "description"=>"<p>A flowchart description of the genetic algorithm applied to a given starting population and controlled by input parameter values. Refer to the text and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000581#pcbi-1000581-g002\" target=\"_blank\">Figure 2</a> for further description of individual steps and parameter definitions.</p>", "links"=>[], "tags"=>["flowchart", "algorithm"], "article_id"=>544332, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Algorithmic_flowchart_of_the_genetic_algorithm_in_SCUEAL_/544332", "title"=>"Algorithmic flowchart of the genetic algorithm in SCUEAL.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:12:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/874460"], "description"=>"<p>An instance when a sequence unclassified by REGA is inferred to be a novel recombinant form by SCUEAL; the A–J mosaic structure is also confirmed by trees and bootscan plots based on the REGA reference alignment.</p>", "links"=>[], "tags"=>["unclassified", "rega", "inferred", "recombinant", "mosaic", "confirmed", "trees", "bootscan", "plots"], "article_id"=>544901, "categories"=>["Infectious Diseases", "Medicine", "Mathematics", "Cancer", "Virology"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581.g007", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_instance_when_a_sequence_unclassified_by_REGA_is_inferred_to_be_a_novel_recombinant_form_by_SCUEAL_the_A_8211_J_mosaic_structure_is_also_confirmed_by_trees_and_bootscan_plots_based_on_the_REGA_reference_alignment_/544901", "title"=>"An instance when a sequence unclassified by REGA is inferred to be a novel recombinant form by SCUEAL; the A–J mosaic structure is also confirmed by trees and bootscan plots based on the REGA reference alignment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-26 01:21:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/433691"], "description"=>"<div><p>Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (≈5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate, robust and extensible subtyping procedures is clear.</p></div>", "links"=>[], "tags"=>["evolutionary", "model-based", "algorithm", "phylogenetic", "breakpoint", "subtype", "hiv-1"], "article_id"=>145554, "categories"=>["Cancer", "Medicine", "Mathematics"], "users"=>["Sergei L. Kosakovsky Pond", "David Posada", "Eric Stawiski", "Colombe Chappey", "Art F.Y. Poon", "Gareth Hughes", "Esther Fearnhill", "Mike B. Gravenor", "Andrew J. Leigh Brown", "Simon D.W. Frost"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000581", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/An_Evolutionary_Model_Based_Algorithm_for_Accurate_Phylogenetic_Breakpoint_Mapping_and_Subtype_Prediction_in_HIV_1/145554", "title"=>"An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-26 01:32:34"}

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