{"id":"https://openalex.org/W7208748802","doi":"https://doi.org/10.64898/2026.09.03.748783","title":"A large-scale evaluation of tree shape indices reveals potential pitfalls","display_name":"A large-scale evaluation of tree shape indices reveals potential pitfalls","publication_year":2026,"publication_date":"2026-09-04","ids":{"openalex":"https://openalex.org/W7208748802","doi":"https://doi.org/10.64898/2026.09.03.748783"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.03.748783","doi":"https://doi.org/10.64898/2026.09.03.748783","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.03.748783","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.03.748783.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.03.748783.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093887328","display_name":"Luise H\u00e4user","orcid":"https://orcid.org/0009-0008-0454-1185","observed_orcids":["https://orcid.org/0009-0008-0454-1185"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luise H\u00e4user","raw_affiliation_strings":["HITS gGmbH"],"raw_orcid":"https://orcid.org/0009-0008-0454-1185","affiliations":[{"raw_affiliation_string":"HITS gGmbH","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025640090","display_name":"Alexandros Stamatakis","orcid":"https://orcid.org/0000-0003-0353-0691","observed_orcids":["https://orcid.org/0000-0003-0353-0691"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alexandros Stamatakis","raw_affiliation_strings":["HITS gGmbH"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HITS gGmbH","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9291999936103821,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9291999936103821,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.010599999688565731,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.006300000008195639,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree-shape","display_name":"phylogenetic tree shape","score":0.9480000138282776},{"id":"https://openalex.org/keywords/root-placement","display_name":"root placement","score":0.6949999928474426},{"id":"https://openalex.org/keywords/index-correlation","display_name":"index correlation","score":0.5379999876022339},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"phylogenomics","score":0.5709999799728394}],"concepts":[{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6636999845504761},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6270999908447266},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.6204000115394592},{"id":"https://openalex.org/C169345407","wikidata":"https://www.wikidata.org/wiki/Q8216221","display_name":"Uncorrelated","level":2,"score":0.5306000113487244},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.5245000123977661},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.38600000739097595},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3346000015735626},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.32409998774528503},{"id":"https://openalex.org/C120936955","wikidata":"https://www.wikidata.org/wiki/Q2155640","display_name":"Empirical research","level":2,"score":0.32199999690055847},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.31279999017715454},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3075000047683716},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29269999265670776},{"id":"https://openalex.org/C100560664","wikidata":"https://www.wikidata.org/wiki/Q3608019","display_name":"K-ary tree","level":4,"score":0.2856999933719635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2777000069618225},{"id":"https://openalex.org/C68775195","wikidata":"https://www.wikidata.org/wiki/Q818944","display_name":"Range tree","level":5,"score":0.25859999656677246},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.2524000108242035},{"id":"https://openalex.org/C207821765","wikidata":"https://www.wikidata.org/wiki/Q405372","display_name":"Instability","level":2,"score":0.25029999017715454}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.03.748783","doi":"https://doi.org/10.64898/2026.09.03.748783","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.03.748783","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.03.748783.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.03.748783","doi":"https://doi.org/10.64898/2026.09.03.748783","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.03.748783","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/04/2026.09.03.748783.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G40230781","display_name":"Strengthening Computational Biodiversity Research in Greece","funder_award_id":"101087081","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320324316","display_name":"Klaus Tschira Stiftung","ror":"https://ror.org/052jep661"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7208748802.pdf","grobid_xml":"https://content.openalex.org/works/W7208748802.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1576649281","https://openalex.org/W1968393777","https://openalex.org/W1971844251","https://openalex.org/W1973194611","https://openalex.org/W1974297141","https://openalex.org/W1980901426","https://openalex.org/W1989243075","https://openalex.org/W1992388733","https://openalex.org/W2002717190","https://openalex.org/W2004149254","https://openalex.org/W2004848466","https://openalex.org/W2029973096","https://openalex.org/W2044441599","https://openalex.org/W2048405441","https://openalex.org/W2054492381","https://openalex.org/W2089563386","https://openalex.org/W2094647384","https://openalex.org/W2095581856","https://openalex.org/W2097487570","https://openalex.org/W2105923020","https://openalex.org/W2109312919","https://openalex.org/W2110891726","https://openalex.org/W2114369768","https://openalex.org/W2114850508","https://openalex.org/W2121815450","https://openalex.org/W2135869163","https://openalex.org/W2138140955","https://openalex.org/W2156524622","https://openalex.org/W2162264429","https://openalex.org/W2163255492","https://openalex.org/W2167696643","https://openalex.org/W2168181417","https://openalex.org/W2277953252","https://openalex.org/W2284241588","https://openalex.org/W2295124130","https://openalex.org/W2321649768","https://openalex.org/W2331613197","https://openalex.org/W2415398545","https://openalex.org/W2518041771","https://openalex.org/W2763425794","https://openalex.org/W2923291801","https://openalex.org/W2949867654","https://openalex.org/W3005235420","https://openalex.org/W3009362918","https://openalex.org/W3019047253","https://openalex.org/W3082596272","https://openalex.org/W3108711400","https://openalex.org/W3118235285","https://openalex.org/W3157396199","https://openalex.org/W3159105183","https://openalex.org/W3188615782","https://openalex.org/W3198283169","https://openalex.org/W3213193750","https://openalex.org/W4205327172","https://openalex.org/W4205916022","https://openalex.org/W4226236648","https://openalex.org/W4360999444","https://openalex.org/W4398796180","https://openalex.org/W4401360550","https://openalex.org/W4407772299","https://openalex.org/W4417227801","https://openalex.org/W6926381661"],"related_works":["https://openalex.org/W4385070997","https://openalex.org/W3202756413","https://openalex.org/W7148204410","https://openalex.org/W3022360965","https://openalex.org/W4407772299","https://openalex.org/W3005144180","https://openalex.org/W2426377470","https://openalex.org/W7098510657","https://openalex.org/W2990919038","https://openalex.org/W2142562060"],"abstract_inverted_index":{"Abstract":[0],"While":[1],"there":[2,75],"exists":[3],"a":[4,14,115,162,194,232,240],"plethora":[5],"of":[6,17,20,69,100,118,143,169,183,202,213],"prior":[7],"research":[8],"on":[9,23,39,246],"phylogenetic":[10],"tree":[11,82,137,152,164,196,215,236],"shape":[12,83,138,165,197,216,237],"indices,":[13,56],"largescale":[15],"analysis":[16],"the":[18,47,55,98,101,122,132,141,214,225],"behavior":[19],"these":[21],"indices":[22,38,87,106,125,147,184,204,263],"empirical":[24,43,247],"trees":[25,44,168],"has":[26],"not":[27,174],"yet":[28],"been":[29],"conducted.":[30],"Here,":[31],"we":[32,57,88,113,256],"address":[33],"this":[34],"by":[35],"computing":[36],"54":[37],"more":[40,241],"than":[41],"45,000,000":[42],"retrieved":[45],"from":[46,250],"EvoNAPS":[48],"and":[49,243,264],"RAxML":[50],"Grove":[51],"databases.":[52],"To":[53],"calculate":[54],"use":[58],"our":[59,70,251],"novel,":[60],"comprehensive":[61,244],"open-source":[62,252],"Python":[63,254],"library":[64],"called":[65],"treeshapy.":[66],"The":[67],"results":[68,223],"large-scale":[71],"evaluation":[72],"indicate":[73],"that":[74,92,110,180],"exist":[76],"several":[77,181],"potential":[78],"pitfalls":[79],"when":[80,156],"conducting":[81,235],"studies.":[84],"For":[85],"14":[86],"find":[89],"clear":[90],"indications,":[91],"they":[93],"are":[94,148,185],"highly":[95],"sensitive":[96],"to":[97,131,192,208],"position":[99],"tree\u2019s":[102],"root.":[103],"Only":[104],"5":[105,146],"appear":[107],"stable":[108],"in":[109,239],"sense,":[111],"while":[112,219],"observe":[114,179],"medium":[116],"degree":[117],"rooting":[119],"instability":[120],"for":[121,167,234,260],"remaining":[123],"35":[124],"under":[126],"study.":[127],"Therefore,":[128],"uncertainties":[129],"pertaining":[130],"root":[133],"placement":[134],"directly":[135],"affect":[136],"values.":[139],"Furthermore,":[140],"values":[142,166],"all":[144],"except":[145],"inherently":[149],"correlated":[150,187],"with":[151,188],"size,":[153],"even":[154],"so,":[155],"applying":[157],"adequate":[158],"normalization":[159],"techniques.":[160],"As":[161],"consequence,":[163],"different":[170],"sizes":[171],"should":[172,205],"generally":[173],"be":[175,206],"compared.":[176],"We":[177],"further":[178],"groups":[182],"strongly":[186],"one":[189],"another.":[190],"Hence,":[191],"conduct":[193],"representative":[195],"study,":[198],"an":[199],"appropriate":[200,258],"subset":[201],"uncorrelated":[203],"selected":[207],"capture":[209],"as":[210,217,231],"many":[211],"aspects":[212],"possible":[218],"avoiding":[220],"essentially":[221],"redundant":[222],"at":[224],"same":[226],"time.":[227],"Our":[228],"study":[229],"serves":[230],"guide":[233],"studies":[238],"cautious":[242],"manner":[245],"data.":[248],"Apart":[249],"treehshapy":[253],"package,":[255],"devise":[257],"guidelines":[259],"selecting":[261],"suitable":[262],"cautiously":[265],"interpreting":[266],"respective":[267],"results.":[268]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-05T00:00:00"}
