Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W2952299127', 'doi': 'https://doi.org/10.1093/sysbio/syx077', 'title': 'To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods', 'display_name': 'To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods', 'publication_year': 2017, 'publication_date': '2017-09-14', 'ids': {'openalex': 'https://openalex.org/W2952299127', 'doi': 'https://doi.org/10.1093/sysbio/syx077', 'mag': '2952299127', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/29029338'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/sysbio/syx077', 'pdf_url': 'https://academic.oup.com/sysbio/article-pdf/67/2/285/24105597/syx077.pdf', 'source': {'id': 'https://openalex.org/S65478581', 'display_name': 'Systematic Biology', 'issn_l': '1063-5157', 'issn': ['1063-5157', '1076-836X'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'pubmed'], 'open_access': {'is_oa': True, 'oa_status': 'bronze', 'oa_url': 'https://academic.oup.com/sysbio/article-pdf/67/2/285/24105597/syx077.pdf', 'any_repository_has_fulltext': True}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5045334836', 'display_name': 'Erin K. Molloy', 'orcid': 'https://orcid.org/0000-0001-5553-3312'}, 'institutions': [{'id': 'https://openalex.org/I157725225', 'display_name': 'University of Illinois Urbana-Champaign', 'ror': 'https://ror.org/047426m28', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I157725225']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Erin K Molloy', 'raw_affiliation_strings': ['Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA'], 'affiliations': [{'raw_affiliation_string': 'Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA', 'institution_ids': ['https://openalex.org/I157725225']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5032411541', 'display_name': 'Tandy Warnow', 'orcid': 'https://orcid.org/0000-0001-7717-3514'}, 'institutions': [{'id': 'https://openalex.org/I157725225', 'display_name': 'University of Illinois Urbana-Champaign', 'ror': 'https://ror.org/047426m28', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I157725225']}], 'countries': ['US'], 'is_corresponding': True, 'raw_author_name': 'Tandy Warnow', 'raw_affiliation_strings': ['Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA'], 'affiliations': [{'raw_affiliation_string': 'Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA', 'institution_ids': ['https://openalex.org/I157725225']}]}], 'institution_assertions': [], 'countries_distinct_count': 1, 'institutions_distinct_count': 1, 'corresponding_author_ids': ['https://openalex.org/A5032411541'], 'corresponding_institution_ids': ['https://openalex.org/I157725225'], 'apc_list': {'value': 1984, 'currency': 'USD', 'value_usd': 1984, 'provenance': 'doaj'}, 'apc_paid': None, 'fwci': 13.768, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 220, 'citation_normalized_percentile': {'value': 0.999951, 'is_in_top_1_percent': True, 'is_in_top_10_percent': True}, 'cited_by_percentile_year': {'min': 99, 'max': 100}, 'biblio': {'volume': '67', 'issue': '2', 'first_page': '285', 'last_page': '303'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10012', 'display_name': 'Genetic diversity and population structure', 'score': 0.9996, 'subfield': {'id': 'https://openalex.org/subfields/1311', 'display_name': 'Genetics'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, 'topics': [{'id': 'https://openalex.org/T10012', 'display_name': 'Genetic diversity and population structure', 'score': 0.9996, 'subfield': {'id': 'https://openalex.org/subfields/1311', 'display_name': 'Genetics'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, {'id': 'https://openalex.org/T10015', 'display_name': 'Genomics and Phylogenetic Studies', 'score': 0.9983, 'subfield': {'id': 'https://openalex.org/subfields/1312', 'display_name': 'Molecular Biology'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}, {'id': 'https://openalex.org/T12115', 'display_name': 'Genetic and Environmental Crop Studies', 'score': 0.997, 'subfield': {'id': 'https://openalex.org/subfields/1110', 'display_name': 'Plant Science'}, 'field': {'id': 'https://openalex.org/fields/11', 'display_name': 'Agricultural and Biological Sciences'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}], 'keywords': [{'id': 'https://openalex.org/keywords/tree', 'display_name': 'Tree (set theory)', 'score': 0.6182107}], 'concepts': [{'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.85521764}, {'id': 'https://openalex.org/C96250715', 'wikidata': 'https://www.wikidata.org/wiki/Q965330', 'display_name': 'Estimation', 'level': 2, 'score': 0.69258004}, {'id': 'https://openalex.org/C113174947', 'wikidata': 'https://www.wikidata.org/wiki/Q2859736', 'display_name': 'Tree (set theory)', 'level': 2, 'score': 0.6182107}, {'id': 'https://openalex.org/C78458016', 'wikidata': 'https://www.wikidata.org/wiki/Q840400', 'display_name': 'Evolutionary biology', 'level': 1, 'score': 0.44545886}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.3893309}, {'id': 'https://openalex.org/C105795698', 'wikidata': 'https://www.wikidata.org/wiki/Q12483', 'display_name': 'Statistics', 'level': 1, 'score': 0.36807978}, {'id': 'https://openalex.org/C33923547', 'wikidata': 'https://www.wikidata.org/wiki/Q395', 'display_name': 'Mathematics', 'level': 0, 'score': 0.17902833}, {'id': 'https://openalex.org/C114614502', 'wikidata': 'https://www.wikidata.org/wiki/Q76592', 'display_name': 'Combinatorics', 'level': 1, 'score': 0.06571022}, {'id': 'https://openalex.org/C187736073', 'wikidata': 'https://www.wikidata.org/wiki/Q2920921', 'display_name': 'Management', 'level': 1, 'score': 0.0}, {'id': 'https://openalex.org/C162324750', 'wikidata': 'https://www.wikidata.org/wiki/Q8134', 'display_name': 'Economics', 'level': 0, 'score': 0.0}], 'mesh': [{'descriptor_ui': 'D002965', 'descriptor_name': 'Classification', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D049810', 'descriptor_name': 'Genetic Speciation', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D008957', 'descriptor_name': 'Models, Genetic', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D010802', 'descriptor_name': 'Phylogeny', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D002965', 'descriptor_name': 'Classification', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D003198', 'descriptor_name': 'Computer Simulation', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D023281', 'descriptor_name': 'Genomics', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D017421', 'descriptor_name': 'Sequence Analysis', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}], 'locations_count': 3, 'locations': [{'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/sysbio/syx077', 'pdf_url': 'https://academic.oup.com/sysbio/article-pdf/67/2/285/24105597/syx077.pdf', 'source': {'id': 'https://openalex.org/S65478581', 'display_name': 'Systematic Biology', 'issn_l': '1063-5157', 'issn': ['1063-5157', '1076-836X'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1101/149120', 'pdf_url': 'https://www.biorxiv.org/content/biorxiv/early/2017/06/12/149120.full.pdf', 'source': None, 'license': 'cc-by-nc-nd', 'license_id': 'https://openalex.org/licenses/cc-by-nc-nd', 'version': 'submittedVersion', 'is_accepted': False, 'is_published': False}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/29029338', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306525036', 'display_name': 'PubMed', 'issn_l': None, 'issn': None, 'is_oa': False, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}], 'best_oa_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.1093/sysbio/syx077', 'pdf_url': 'https://academic.oup.com/sysbio/article-pdf/67/2/285/24105597/syx077.pdf', 'source': {'id': 'https://openalex.org/S65478581', 'display_name': 'Systematic Biology', 'issn_l': '1063-5157', 'issn': ['1063-5157', '1076-836X'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310311648', 'host_organization_name': 'Oxford University Press', 'host_organization_lineage': ['https://openalex.org/P4310311647', 'https://openalex.org/P4310311648'], 'host_organization_lineage_names': ['University of Oxford', 'Oxford University Press'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'sustainable_development_goals': [], 'grants': [{'funder': 'https://openalex.org/F4320335353', 'funder_display_name': 'National Science Foundation of Sri Lanka', 'award_id': 'ACI-1238993'}, {'funder': 'https://openalex.org/F4320335353', 'funder_display_name': 'National Science Foundation of Sri Lanka', 'award_id': 'OCI-0725070'}], 'datasets': [], 'versions': [], 'referenced_works_count': 118, 'referenced_works': ['https://openalex.org/W1495737144', 'https://openalex.org/W1517039185', 'https://openalex.org/W1593676244', 'https://openalex.org/W1889423108', 'https://openalex.org/W1897064680', 'https://openalex.org/W1902522291', 'https://openalex.org/W1924404512', 'https://openalex.org/W1929783548', 'https://openalex.org/W1972157500', 'https://openalex.org/W1975933692', 'https://openalex.org/W1977099058', 'https://openalex.org/W1980777164', 'https://openalex.org/W1983753237', 'https://openalex.org/W1985092783', 'https://openalex.org/W1988170736', 'https://openalex.org/W2002579489', 'https://openalex.org/W2011606533', 'https://openalex.org/W2012220164', 'https://openalex.org/W2013277649', 'https://openalex.org/W2014087252', 'https://openalex.org/W2015800458', 'https://openalex.org/W2016171324', 'https://openalex.org/W2019182846', 'https://openalex.org/W2030966943', 'https://openalex.org/W2032016329', 'https://openalex.org/W2037654474', 'https://openalex.org/W2041101954', 'https://openalex.org/W2046132104', 'https://openalex.org/W2052432722', 'https://openalex.org/W2060425093', 'https://openalex.org/W2063448278', 'https://openalex.org/W2067677292', 'https://openalex.org/W2075700316', 'https://openalex.org/W2083015817', 'https://openalex.org/W2089929482', 'https://openalex.org/W2096689134', 'https://openalex.org/W2097706568', 'https://openalex.org/W2097831352', 'https://openalex.org/W2097879530', 'https://openalex.org/W2099459260', 'https://openalex.org/W2099593729', 'https://openalex.org/W2099882047', 'https://openalex.org/W2103849916', 'https://openalex.org/W2105541048', 'https://openalex.org/W2106669588', 'https://openalex.org/W2106704226', 'https://openalex.org/W2107608009', 'https://openalex.org/W2108039804', 'https://openalex.org/W2112947508', 'https://openalex.org/W2114227052', 'https://openalex.org/W2116103312', 'https://openalex.org/W2119837484', 'https://openalex.org/W2120663060', 'https://openalex.org/W2123800174', 'https://openalex.org/W2125024684', 'https://openalex.org/W2125971557', 'https://openalex.org/W2127713506', 'https://openalex.org/W2135123683', 'https://openalex.org/W2136353610', 'https://openalex.org/W2138514847', 'https://openalex.org/W2139050004', 'https://openalex.org/W2139146574', 'https://openalex.org/W2139478957', 'https://openalex.org/W2139736670', 'https://openalex.org/W2140966447', 'https://openalex.org/W2141052558', 'https://openalex.org/W2142718629', 'https://openalex.org/W2145562754', 'https://openalex.org/W2145608399', 'https://openalex.org/W2148346591', 'https://openalex.org/W2148723086', 'https://openalex.org/W2148929479', 'https://openalex.org/W2151320514', 'https://openalex.org/W2152293390', 'https://openalex.org/W2152477201', 'https://openalex.org/W2153631698', 'https://openalex.org/W2157019299', 'https://openalex.org/W2157552136', 'https://openalex.org/W2158482855', 'https://openalex.org/W2158952520', 'https://openalex.org/W2159446562', 'https://openalex.org/W2160936843', 'https://openalex.org/W2161444534', 'https://openalex.org/W2162336040', 'https://openalex.org/W2164789250', 'https://openalex.org/W2169773990', 'https://openalex.org/W2170920620', 'https://openalex.org/W2174889714', 'https://openalex.org/W2176256193', 'https://openalex.org/W2176633348', 'https://openalex.org/W2177324599', 'https://openalex.org/W2178890195', 'https://openalex.org/W2179623716', 'https://openalex.org/W2228868916', 'https://openalex.org/W2255592388', 'https://openalex.org/W2263985547', 'https://openalex.org/W2277574918', 'https://openalex.org/W2323303653', 'https://openalex.org/W2338402689', 'https://openalex.org/W2344334426', 'https://openalex.org/W2345610960', 'https://openalex.org/W2346920492', 'https://openalex.org/W2416129936', 'https://openalex.org/W2529349860', 'https://openalex.org/W2529434768', 'https://openalex.org/W2594095179', 'https://openalex.org/W2608378253', 'https://openalex.org/W2610523845', 'https://openalex.org/W2617791656', 'https://openalex.org/W2736094286', 'https://openalex.org/W2947404581', 'https://openalex.org/W2949247626', 'https://openalex.org/W2950111230', 'https://openalex.org/W2950847777', 'https://openalex.org/W2962725223', 'https://openalex.org/W3217097258', 'https://openalex.org/W4229487902', 'https://openalex.org/W789543396'], 'related_works': ['https://openalex.org/W4383503847', 'https://openalex.org/W4249206767', 'https://openalex.org/W4243860260', 'https://openalex.org/W2608353378', 'https://openalex.org/W2576994247', 'https://openalex.org/W2563559453', 'https://openalex.org/W2382330008', 'https://openalex.org/W2342695897', 'https://openalex.org/W1922851888', 'https://openalex.org/W1519970947'], 'abstract_inverted_index': {'With': [0], 'the': [1, 67, 78, 82, 89, 102, 109, 123, 139, 156, 183, 186, 242, 256, 259, 276, 313, 338, 348, 361, 377], 'increasing': [2], 'availability': [3], 'of': [4, 18, 61, 69, 111, 125, 141, 158, 176, 189, 236, 258, 264, 282, 315, 340, 350, 363, 379], 'whole': [5], 'genome': [6], 'data,': [7], 'many': [8, 47, 60, 129], 'species': [9, 32, 56, 83, 90, 103, 127, 150, 159, 190, 358], 'trees': [10, 80], 'are': [11, 63], 'being': [12], 'constructed': [13], 'from': [14, 105, 309], 'hundreds': [15], 'to': [16, 46, 115, 148, 202, 270], 'thousands': [17], 'loci.': [19, 113], 'Although': [20], 'concatenation': [21, 224, 304], 'analysis': [22, 225, 305], 'using': [23, 226, 306], 'maximum': [24, 227], 'likelihood': [25, 228], 'is': [26, 153, 166], 'a': [27, 214, 233], 'standard': [28], 'approach': [29], 'for': [30, 38, 356], 'estimating': [31, 357], 'trees,': [33, 96, 128], 'it': [34], 'does': [35], 'not': [36, 274, 332], 'account': [37], 'gene': [39, 79, 95, 164, 203, 251, 287, 316, 351, 380], 'tree': [40, 57, 91, 104, 160, 191, 252, 288, 317, 359], 'heterogeneity,': [41], 'which': [42, 62], 'can': [43], 'occur': [44], 'due': [45], 'biological': [48], 'processes,': [49], 'such': [50], 'as': [51], 'incomplete': [52, 70, 171, 265, 283, 364], 'lineage': [53, 71, 172, 266, 284, 365], 'sorting.': [54], 'Coalescent': [55], 'estimation': [58, 161, 192, 253, 289, 318], 'methods,': [59], 'statistically': [64], 'consistent': [65], 'in': [66, 108, 360, 373], 'presence': [68, 362], 'sorting,': [72, 173, 285], 'include': [73], 'Bayesian': [74], 'methods': [75, 86, 99, 162, 193, 209, 261, 278], 'that': [76, 87, 100, 117], 'coestimate': [77], 'and': [81, 97, 179, 185, 194, 212, 221, 241, 367], 'tree,': [84], 'summary': [85, 208, 260, 277], 'compute': [88], 'by': [92], 'combining': [93], 'estimated': [94, 126], 'site-based': [98, 215], 'infer': [101], 'site': [106], 'patterns': [107], 'alignments': [110], 'different': [112], 'Due': [114], 'concerns': [116], 'poor': [118], 'quality': [119], 'loci': [120], 'will': [121], 'reduce': [122], 'accuracy': [124, 188, 257, 339], 'recent': [130], 'phylogenomic': [131], 'studies': [132, 375], 'have': [133], 'removed': [134], 'or': [135, 335], 'filtered': [136], 'genes': [137, 248, 311, 322], 'on': [138, 232, 250, 312, 324], 'basis': [140, 314], 'phylogenetic': [142, 174], 'signal': [143, 175], 'and/or': [144], 'missing': [145, 180, 325], 'data': [146, 181, 239, 326], 'prior': [147, 374], 'inferring': [149], 'trees;': [151], 'little': [152], 'known': [154], 'about': [155], 'performance': [157], 'when': [163, 262], 'filtering': [165, 204, 310, 321], 'performed.': [167], 'We': [168], 'examine': [169], 'how': [170, 196], 'individual': [177], 'loci,': [178], 'affect': [182, 199], 'absolute': [184], 'relative': [187], 'show': [195], 'these': [197], 'properties': [198], "methods'": [200], 'responses': [201], 'strategies.': [205], 'In': [206], 'particular,': [207], '(ASTRAL-II,': [210], 'ASTRID,': [211], 'MP-EST),': [213], 'coalescent': [216], 'method': [217], '(SVDquartets': [218], 'within': [219], 'PAUP*),': [220], 'an': [222], 'unpartitioned': [223], '(RAxML)': [229], 'were': [230, 245, 268], 'evaluated': [231], 'heterogeneous': [234], 'collection': [235], 'simulated': [237], 'multilocus': [238], 'sets,': [240], 'following': [243], 'trends': [244], 'observed.': [246], 'Filtering': [247], 'based': [249, 323], 'error': [254, 290], 'improved': [255], 'levels': [263, 281], 'sorting': [267, 366], 'low': [269], 'moderate': [271], 'but': [272], 'did': [273, 331], 'benefit': [275], 'under': [279], 'higher': [280], 'unless': [286], 'was': [291, 327], 'also': [292], 'extremely': [293], 'high': [294], '(a': [295], 'model': [296], 'condition': [297], 'with': [298], 'few': [299], 'replicates).': [300], 'Neither': [301], 'SVDquartets': [302], 'nor': [303], 'RAxML': [307], 'benefited': [308], 'error.': [319], 'Finally,': [320], 'either': [328], 'neutral': [329], '(i.e.,': [330], 'impact': [333, 378], 'accuracy)': [334], 'else': [336], 'reduced': [337], 'all': [341], 'five': [342], 'methods.': [343], 'By': [344], 'providing': [345], 'insight': [346], 'into': [347], 'consequences': [349], 'filtering,': [352], 'we': [353], 'offer': [354], 'recommendations': [355], 'reconcile': [368], 'seemingly': [369], 'conflicting': [370], 'observations': [371], 'made': [372], 'regarding': [376], 'filtering.': [381]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2952299127', 'counts_by_year': [{'year': 2024, 'cited_by_count': 20}, {'year': 2023, 'cited_by_count': 29}, {'year': 2022, 'cited_by_count': 34}, {'year': 2021, 'cited_by_count': 56}, {'year': 2020, 'cited_by_count': 35}, {'year': 2019, 'cited_by_count': 23}, {'year': 2018, 'cited_by_count': 22}, {'year': 2017, 'cited_by_count': 1}], 'updated_date': '2024-12-30T10:01:08.813814', 'created_date': '2019-06-27'}