Rec-DCM-Eigen: Reconstructing a Less Parsimonious but More Accurate Tree in Shorter Time
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{"title"=>"Rec-DCM-Eigen: Reconstructing a less parsimonious but more accurate tree in shorter time", "type"=>"journal", "authors"=>[{"first_name"=>"Seunghwa", "last_name"=>"Kang", "scopus_author_id"=>"56119943700"}, {"first_name"=>"Jijun", "last_name"=>"Tang", "scopus_author_id"=>"8948124600"}, {"first_name"=>"Stephen W.", "last_name"=>"Schaeffer", "scopus_author_id"=>"7005625304"}, {"first_name"=>"David A.", "last_name"=>"Bader", "scopus_author_id"=>"7102450485"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-80051958815", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "pmid"=>"21887219", "issn"=>"19326203", "sgr"=>"80051958815", "doi"=>"10.1371/journal.pone.0022483", "pui"=>"362405466"}, "id"=>"2932d214-9344-3692-8697-d68b92e12fd5", "abstract"=>"Maximum parsimony (MP) methods aim to reconstruct the phylogeny of extant species by finding the most parsimonious evolutionary scenario using the species' genome data. MP methods are considered to be accurate, but they are also computationally expensive especially for a large number of species. Several disk-covering methods (DCMs), which decompose the input species to multiple overlapping subgroups (or disks), have been proposed to solve the problem in a divide-and-conquer way. We design a new DCM based on the spectral method and also develop the COGNAC (Comparing Orders of Genes using Novel Algorithms and high-performance Computers) software package. COGNAC uses the new DCM to reduce the phylogenetic tree search space and selects an output tree from the reduced search space based on the MP principle. We test the new DCM using gene order data and inversion distance. The new DCM not only reduces the number of candidate tree topologies but also excludes erroneous tree topologies which can be selected by original MP methods. Initial labeling of internal genomes affects the accuracy of MP methods using gene order data, and the new DCM enables more accurate initial labeling as well. COGNAC demonstrates superior accuracy as a consequence. We compare COGNAC with FastME and the combination of the state of the art DCM (Rec-I-DCM3) and GRAPPA. COGNAC clearly outperforms FastME in accuracy. COGNAC--using the new DCM--also reconstructs a much more accurate tree in significantly shorter time than GRAPPA with Rec-I-DCM3.", "link"=>"http://www.mendeley.com/research/recdcmeigen-reconstructing-less-parsimonious-more-accurate-tree-shorter-time", "reader_count"=>11, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Agricultural and Biological Sciences"=>8, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Computer Science"=>{"Computer Science"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Argentina"=>1, "United States"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/742517"], "description"=>"<p>The figure depicts a model tree adopted from a biology paper <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022483#pone.0022483-Bhutkar1\" target=\"_blank\">[20]</a>.</p>", "links"=>[], "tags"=>["superiority", "initializing"], "article_id"=>412894, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g007", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_model_tree_used_to_demonstrate_the_superiority_of_COGNAC_in_initializing_internal_nodes_/412894", "title"=>"A model tree used to demonstrate the superiority of <i>COGNAC</i> in initializing internal nodes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:24:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/742304"], "description"=>"<p>The trees above show the phylogenetic relationships of twelve genomes. The value next to a genome name is the genome's eigenvector element computed using (top), (middle), and (bottom), respectively.</p>", "links"=>[], "tags"=>["Computational biology", "computer science"], "article_id"=>412682, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_showing_an_advantage_of_using_and_over_/412682", "title"=>"An example showing an advantage of using and over .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:23:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/742199"], "description"=>"<p>An overview of the new DCM.</p>", "links"=>[], "tags"=>["overview"], "article_id"=>412570, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_overview_of_the_new_DCM_/412570", "title"=>"An overview of the new DCM.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:22:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/742683"], "description"=>"<p>We generate 10 model trees for a given number of genomes (). The number of false positives (FP), the number of false negatives (FN), and the execution time (time) in a cell are the average of the finished computations (finished: the number of finished computations within 24 hours) out of 10 trials using 10 different model trees. , , and in the tables are hours, minutes, and seconds, respectively. is the number of genes in a genome, which is 100 in our experiments.</p>", "links"=>[], "tags"=>["birth-death", "trees", "diameter", "lengths", "skewed"], "article_id"=>413060, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.t003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_results_for_birth_death_trees_with_the_diameter_of_1_and_edge_lengths_in_a_skewed_distribution_/413060", "title"=>"Experimental results for birth-death trees with the diameter of 1 and edge lengths in a skewed distribution.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 15:25:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/742715"], "description"=>"<p>We generate 10 model trees for a given number of genomes (). The number of false positives (FP), the number of false negatives (FN), and the execution time (time) in a cell are the average of the finished computations (finished: the number of finished computations within 24 hours) out of 10 trials using 10 different model trees. , , and in the tables are hours, minutes, and seconds, respectively.</p>", "links"=>[], "tags"=>["birth-death", "trees", "lengths"], "article_id"=>413094, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_results_for_birth_death_trees_with_the_edge_lengths_between_0_and_16_/413094", "title"=>"Experimental results for birth-death trees with the edge lengths between 0 and 16.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 15:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/742475"], "description"=>"<p>Numbers on top of edges are edge lengths.</p>", "links"=>[], "tags"=>["reconstructed", "trees", "mp", "grappa"], "article_id"=>412847, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_model_tree_left_and_two_reconstructed_trees_using_an_original_MP_method_the_GRAPPA_method_center_and_COGNAC_right_/412847", "title"=>"A model tree (left) and two reconstructed trees using an original MP method (the GRAPPA method) (center) and <i>COGNAC</i> (right).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:24:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/742247"], "description"=>"<p>An incompatible but recoverable disk decomposition.</p>", "links"=>[], "tags"=>["incompatible", "recoverable"], "article_id"=>412626, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_incompatible_but_recoverable_disk_decomposition_/412626", "title"=>"An incompatible but recoverable disk decomposition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:23:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/742562"], "description"=>"<p>The figures plot (FP+FN)/2 (FP is the number of false positives and FN is the number of false negatives) for a varying number of genomes (20, 40, 80, 160, 320, 640). The numbers are the average of the finished computations. Missing points indicate that no computation finished within 24 hours. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022483#pone-0022483-t001\" target=\"_blank\">Tables 1</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022483#pone-0022483-t002\" target=\"_blank\">2</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022483#pone-0022483-t003\" target=\"_blank\">3</a>, and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022483#pone-0022483-t004\" target=\"_blank\">4</a> for additional details.</p>", "links"=>[], "tags"=>["Computational biology", "computer science"], "article_id"=>412938, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g008", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_summary_of_the_experimental_results_/412938", "title"=>"A summary of the experimental results.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:24:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/742657"], "description"=>"<p>We generate 10 model trees for a given number of genomes (). The number of false positives (FP), the number of false negatives (FN), and the execution time (time) in a cell are the average of the finished computations (finished: the number of finished computations within 24 hours) out of 10 trials using 10 different model trees. , , and in the tables are hours, minutes, and seconds, respectively.</p>", "links"=>[], "tags"=>["uniform-random", "trees", "lengths"], "article_id"=>413028, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_results_for_uniform_random_trees_with_the_edge_lengths_between_0_and_16_/413028", "title"=>"Experimental results for uniform-random trees with the edge lengths between 0 and 16.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 15:25:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/742750"], "description"=>"<p>We generate 10 model trees for a given number of genomes (). The number of false positives (FP), the number of false negatives (FN), and the execution time (time) in a cell are the average of the finished computations (finished: the number of finished computations within 24 hours) out of 10 trials using 10 different model trees. , , and in the tables are hours, minutes, and seconds, respectively. is the number of genes in a genome, which is 100 in our experiments.</p>", "links"=>[], "tags"=>["birth-death", "trees", "diameter", "lengths", "skewed"], "article_id"=>413121, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.t004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_results_for_birth_death_trees_with_the_diameter_of_2_and_edge_lengths_in_a_skewed_distribution_/413121", "title"=>"Experimental results for birth-death trees with the diameter of 2 and edge lengths in a skewed distribution.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 15:25:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/742414"], "description"=>"<p>The tree above depicts the phylogenetic relationships of the input genomes and the eigenvector element computed using follows a genome name. Two long edges separate A0 and A1 and C0 and C1 from the remaining genomes in the center. The eigenvector elements for the genomes in the center are very small.</p>", "links"=>[], "tags"=>["illustrating", "heuristic", "placing", "genomes", "overlapping"], "article_id"=>412786, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_illustrating_the_necessity_of_a_heuristic_to_avoid_placing_a_large_number_of_genomes_in_the_overlapping_region_/412786", "title"=>"An example illustrating the necessity of a heuristic to avoid placing a large number of genomes in the overlapping region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:24:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/742357"], "description"=>"<p>The trees above show the phylogenetic relationships of five genomes. The value next to a genome name is the genome's eigenvector element computed using (top) and (bottom), respectively.</p>", "links"=>[], "tags"=>["Computational biology", "computer science"], "article_id"=>412735, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Seunghwa Kang", "Jijun Tang", "Stephen W. Schaeffer", "David A. Bader"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022483.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_showing_an_advantage_of_using_over_/412735", "title"=>"An example showing an advantage of using over .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 15:23:46"}

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Relative Metric

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