Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation

Motivation The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being su...

Ausführliche Beschreibung

Gespeichert in:

Bibliographische Detailangaben
Veröffentlicht in:	Bioinformatics (Oxford, England) Jg. 40; H. 3
Hauptverfasser:	Ferreiro, David, Branco, Catarina, Arenas, Miguel
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	England Oxford University Press 04.03.2024 Oxford Publishing Limited (England)
Schlagworte:	Availability Bayes Theorem Bayesian analysis Computation Constraints Evolution Evolution, Molecular Graphical user interface Likelihood Functions Mathematical models Models, Genetic Molecular evolution Molecular modelling Original Paper Phylogeny Protein families Proteins Proteins - genetics Substitutes
ISSN:	1367-4803, 1367-4811, 1367-4811
Online-Zugang:	Volltext
Tags:	Tag hinzufügen Keine Tags, Fügen Sie den ersten Tag hinzu!

Abstract	Motivation The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection. Results We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models. Availability and implementation ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples.
AbstractList	The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection. We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models. ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples. Motivation The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection. Results We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models. Availability and implementation ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples. The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection.MOTIVATIONThe selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection.We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models.RESULTSWe present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models.ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples.AVAILABILITY AND IMPLEMENTATIONProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples. Motivation The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection. Results We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models. Availability and implementation ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples.
Author	Branco, Catarina Ferreiro, David Arenas, Miguel
Author_xml	– sequence: 1 givenname: David surname: Ferreiro fullname: Ferreiro, David – sequence: 2 givenname: Catarina surname: Branco fullname: Branco, Catarina – sequence: 3 givenname: Miguel orcidid: 0000-0002-0516-2717 surname: Arenas fullname: Arenas, Miguel email: marenas@uvigo.es
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/38374231$$D View this record in MEDLINE/PubMed
BookMark	eNqNUk1vFSEUJaaN_dC_0JC4cTMWBmZgVkYbv5ImXahrwsCdSjMDIx-Nb-8Pl-d7vtiuuoJ77zkn58A9Q0c-eEDogpI3lAzscnTB-SnERWdn0uWYNZChf4ZOKetFwyWlR4c7YSfoLKU7QkhHuv45OmGSCd4yeop-f4UZTHbBY70Ef4uTy9BYWMFb8BmnHIvJJep53mATfK2182BxKmPKLpe_1CVYmBMOE15jyOA8hvsw72bjBuu1tn-56hXwe72B5LSvYstast5iXqDjSc8JXu7Pc_T944dvV5-b65tPX67eXTeGszY3duQg-qkjlgtiuwGIHpnhsjfUClJzCiGMBjG2xgAzZKBTW0vd9VQaYzU7R293umsZF7CmBqzB1BqrtbhRQTv1cOLdD3Ub7lV9csp5J6vC671CDD8LpKwWlwzMs_YQSlLt0ErZcdFuoa8eQe9Cib7mU6ylrJOS8S3q4n9LBy__fqgC-h3AxJBShOkAoWTri6mHq6D2q1CJdEcMZX0q5w-eH8RE
Cites_doi	10.1093/bioinformatics/btr088 10.1093/molbev/msg184 10.1093/bioinformatics/btt530 10.1126/science.185.4154.862 10.1534/genetics.109.109058 10.1093/molbev/msl015 10.1038/379096a0 10.1093/ve/veaa066 10.1186/1471-2148-10-99 10.1093/molbev/msab120 10.1073/pnas.0501865102 10.1371/journal.pcbi.0030052 10.1016/j.csbj.2020.11.007 10.1073/pnas.1412933112 10.1089/cmb.2019.0500 10.1093/bioinformatics/btz305 10.1038/nrg.2015.18 10.1093/oxfordjournals.molbev.a003851 10.1002/prot.24244 10.1093/oxfordjournals.molbev.a025888 10.1093/ve/veac115 10.1038/s41580-019-0163-x 10.1080/10635150490423520 10.1093/molbev/msq168 10.3389/fgene.2015.00319 10.1007/s00239-015-9673-0 10.1093/bioinformatics/8.3.275 10.1093/molbev/msv085 10.1016/0014-5793(83)80731-5 10.1371/journal.pone.0143245 10.1093/molbev/msac231 10.1371/journal.pcbi.1002803 10.1093/gbe/evt110 10.1016/0304-4149(82)90011-4 10.1093/nar/gkh340 10.1007/s00239-001-2304-y 10.1089/10665270050514918 10.1038/s41586-021-03819-2 10.1016/j.gene.2004.12.011 10.1007/PL00000067 10.1016/S0959-437X(00)00142-8 10.1016/j.virol.2014.01.029 10.1109/TCBB.2017.2784434 10.1002/pro.2071 10.1093/acprof:oso/9780198567028.001.0001 10.3390/genes13020384 10.1093/molbev/mst178 10.1038/s41598-017-03260-4 10.4081/eb.2012.e9 10.1093/sysbio/syz022 10.1080/10635150390235494 10.1093/molbev/msu411 10.1073/pnas.89.22.10915 10.1093/molbev/msn067 10.1093/gbe/evr080 10.1093/molbev/msac144 10.1371/journal.pgen.1008711 10.1093/nar/gks1067 10.1093/molbev/msy244 10.1186/1471-2148-6-29 10.1007/s002399910038 10.1093/molbev/msz189 10.1093/molbev/msp146 10.1038/hdy.2013.101 10.1093/molbev/msj102 10.1038/hdy.2011.116 10.7717/peerj.5549 10.1093/molbev/msi005 10.1371/journal.pcbi.1002495 10.1093/molbev/mst240 10.1093/genetics/162.4.2025 10.1038/s41559-017-0338-9 10.1146/annurev-ecolsys-102209-144621 10.1093/nar/gkaa913 10.1093/molbev/msz122 10.1093/oxfordjournals.molbev.a026171 10.1038/nrg3130 10.1002/prot.20240 10.1016/j.gene.2004.12.015 10.1146/annurev.ecolsys.36.102003.152633 10.1016/j.gene.2023.147336 10.1371/journal.pcbi.1000592 10.1093/molbev/msn264 10.1093/molbev/msl136 10.1038/nmeth.4285 10.32614/RJ-2015-030 10.1002/pro.2897 10.1007/s11222-009-9116-0 10.1006/jmbi.1994.1190 10.1093/bioinformatics/bti770 10.1093/molbev/msq196 10.1038/s43588-021-00098-9 10.1186/1471-2148-10-242 10.1093/bioinformatics/btab617 10.1093/molbev/msac063 10.1111/j.2041-210X.2011.00179.x 10.1371/journal.pone.0000503 10.1007/s00239-022-10080-2 10.1111/2041-210X.13341 10.1093/bioinformatics/18.suppl_1.S71 10.1002/prot.22964 10.1126/science.abj8754 10.1016/j.ympev.2013.03.030 10.1016/j.meegid.2020.104646
ContentType	Journal Article
Copyright	The Author(s) 2024. Published by Oxford University Press. 2024 The Author(s) 2024. Published by Oxford University Press.
Copyright_xml	– notice: The Author(s) 2024. Published by Oxford University Press. 2024 – notice: The Author(s) 2024. Published by Oxford University Press.
DBID	TOX AAYXX CITATION CGR CUY CVF ECM EIF NPM 7QF 7QO 7QQ 7SC 7SE 7SP 7SR 7TA 7TB 7TM 7TO 7U5 8BQ 8FD F28 FR3 H8D H8G H94 JG9 JQ2 K9. KR7 L7M L~C L~D P64 7X8 5PM
DOI	10.1093/bioinformatics/btae096
DatabaseName	Oxford Journals Open Access Collection CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed Aluminium Industry Abstracts Biotechnology Research Abstracts Ceramic Abstracts Computer and Information Systems Abstracts Corrosion Abstracts Electronics & Communications Abstracts Engineered Materials Abstracts Materials Business File Mechanical & Transportation Engineering Abstracts Nucleic Acids Abstracts Oncogenes and Growth Factors Abstracts Solid State and Superconductivity Abstracts METADEX Technology Research Database ANTE: Abstracts in New Technology & Engineering Engineering Research Database Aerospace Database Copper Technical Reference Library AIDS and Cancer Research Abstracts Materials Research Database ProQuest Computer Science Collection ProQuest Health & Medical Complete (Alumni) Civil Engineering Abstracts Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional Biotechnology and BioEngineering Abstracts MEDLINE - Academic PubMed Central (Full Participant titles)
DatabaseTitle	CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Materials Research Database Oncogenes and Growth Factors Abstracts Technology Research Database Computer and Information Systems Abstracts – Academic Mechanical & Transportation Engineering Abstracts Nucleic Acids Abstracts ProQuest Computer Science Collection Computer and Information Systems Abstracts ProQuest Health & Medical Complete (Alumni) Materials Business File Aerospace Database Copper Technical Reference Library Engineered Materials Abstracts Biotechnology Research Abstracts AIDS and Cancer Research Abstracts Advanced Technologies Database with Aerospace ANTE: Abstracts in New Technology & Engineering Civil Engineering Abstracts Aluminium Industry Abstracts Electronics & Communications Abstracts Ceramic Abstracts METADEX Biotechnology and BioEngineering Abstracts Computer and Information Systems Abstracts Professional Solid State and Superconductivity Abstracts Engineering Research Database Corrosion Abstracts MEDLINE - Academic
DatabaseTitleList	MEDLINE Materials Research Database MEDLINE - Academic
Database_xml	– sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: TOX name: Oxford Journals Open Access Collection url: https://academic.oup.com/journals/ sourceTypes: Publisher – sequence: 3 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Biology
EISSN	1367-4811
ExternalDocumentID	PMC10914458 38374231 10_1093_bioinformatics_btae096 10.1093/bioinformatics/btae096
Genre	Research Support, Non-U.S. Gov't Journal Article
GrantInformation_xml	– fundername: Spanish Ministry of Science and Innovation – fundername: Xunta de Galicia grantid: ED481A-2020/192 – fundername: ; – fundername: ; grantid: ED481A-2020/192
GroupedDBID	--- -E4 -~X .-4 .2P .DC .GJ .I3 0R~ 1TH 23N 2WC 4.4 48X 53G 5GY 5WA 70D AAIJN AAIMJ AAJKP AAJQQ AAKPC AAMDB AAMVS AAOGV AAPQZ AAPXW AAUQX AAVAP AAVLN ABEFU ABEJV ABEUO ABGNP ABIXL ABNGD ABNKS ABPQP ABPTD ABQLI ABWST ABXVV ABZBJ ACGFS ACIWK ACPRK ACUFI ACUKT ACUXJ ACYTK ADBBV ADEYI ADEZT ADFTL ADGKP ADGZP ADHKW ADHZD ADMLS ADOCK ADPDF ADRDM ADRTK ADVEK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFNX AFFZL AFGWE AFIYH AFOFC AFRAH AGINJ AGKEF AGQPQ AGQXC AGSYK AHMBA AHXPO AI. AIJHB AJEEA AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC AMNDL APIBT APWMN AQDSO ARIXL ASPBG ATTQO AVWKF AXUDD AYOIW AZFZN AZVOD BAWUL BAYMD BHONS BQDIO BQUQU BSWAC BTQHN C1A C45 CAG CDBKE COF CS3 CZ4 DAKXR DIK DILTD DU5 D~K EBD EBS EE~ EJD ELUNK EMOBN F5P F9B FEDTE FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GROUPED_DOAJ GX1 H13 H5~ HAR HVGLF HW0 HZ~ IOX J21 JXSIZ KAQDR KOP KQ8 KSI KSN M-Z MK~ ML0 N9A NGC NLBLG NMDNZ NOMLY NTWIH NU- NVLIB O0~ O9- OAWHX ODMLO OJQWA OK1 OVD OVEED O~Y P2P PAFKI PB- PEELM PQQKQ Q1. Q5Y R44 RD5 RIG RNI RNS ROL RPM RUSNO RW1 RXO RZF RZO SV3 TEORI TJP TLC TOX TR2 VH1 W8F WOQ X7H YAYTL YKOAZ YXANX ZGI ZKX ~91 ~KM AAYXX CITATION ROX CGR CUY CVF ECM EIF NPM 7QF 7QO 7QQ 7SC 7SE 7SP 7SR 7TA 7TB 7TM 7TO 7U5 8BQ 8FD F28 FR3 H8D H8G H94 JG9 JQ2 K9. KR7 L7M L~C L~D P64 7X8 5PM
ID	FETCH-LOGICAL-c432t-db4e76f50d470d59e0ab3c486c1d70480777cae7b2cce3c091f2ae7a5618ccda3
IEDL.DBID	TOX
ISICitedReferencesCount	4
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001178651800002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	1367-4803 1367-4811
IngestDate	Thu Aug 21 18:35:32 EDT 2025 Fri Jul 11 14:22:17 EDT 2025 Fri Oct 03 11:20:19 EDT 2025 Mon Jul 21 05:54:13 EDT 2025 Sat Nov 29 03:49:29 EST 2025 Mon Jun 30 08:34:48 EDT 2025
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	3
Language	English
License	This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. https://creativecommons.org/licenses/by/4.0 The Author(s) 2024. Published by Oxford University Press.
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c432t-db4e76f50d470d59e0ab3c486c1d70480777cae7b2cce3c091f2ae7a5618ccda3
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ORCID	0000-0002-0516-2717
OpenAccessLink	https://dx.doi.org/10.1093/bioinformatics/btae096
PMID	38374231
PQID	3213588348
PQPubID	36124
ParticipantIDs	pubmedcentral_primary_oai_pubmedcentral_nih_gov_10914458 proquest_miscellaneous_2928854728 proquest_journals_3213588348 pubmed_primary_38374231 crossref_primary_10_1093_bioinformatics_btae096 oup_primary_10_1093_bioinformatics_btae096
PublicationCentury	2000
PublicationDate	2024-03-04
PublicationDateYYYYMMDD	2024-03-04
PublicationDate_xml	– month: 03 year: 2024 text: 2024-03-04 day: 04
PublicationDecade	2020
PublicationPlace	England
PublicationPlace_xml	– name: England – name: Oxford
PublicationTitle	Bioinformatics (Oxford, England)
PublicationTitleAlternate	Bioinformatics
PublicationYear	2024
Publisher	Oxford University Press Oxford Publishing Limited (England)
Publisher_xml	– name: Oxford University Press – name: Oxford Publishing Limited (England)
References	Arenas (2024030523340944000_btae096-B10) 2013; 29 Hoban (2024030523340944000_btae096-B51) 2012; 13 Sigrist (2024030523340944000_btae096-B94) 2012; 41 Kosiol (2024030523340944000_btae096-B60) 2005; 22 Blum (2024030523340944000_btae096-B22) 2010; 20 Rodrigue (2024030523340944000_btae096-B89) 2005; 347 Dimmic (2024030523340944000_btae096-B37) 2002; 55 Shakhnovich (2024030523340944000_btae096-B92) 1996; 379 Jiménez-Santos (2024030523340944000_btae096-B52) 2018; 6 Arenas (2024030523340944000_btae096-B9) 2019; 11 Codoñer (2024030523340944000_btae096-B27) 2017; 7 Minin (2024030523340944000_btae096-B70) 2003; 52 Perron (2024030523340944000_btae096-B82) 2019; 36 Cox (2024030523340944000_btae096-B28) 2013; 68 Sella (2024030523340944000_btae096-B90) 2005; 102 Abascal (2024030523340944000_btae096-B1) 2007; 24 Arenas (2024030523340944000_btae096-B13) 2017; 66 Franzosa (2024030523340944000_btae096-B43) 2009; 26 Dang (2024030523340944000_btae096-B30) 2010; 10 Arnold (2024030523340944000_btae096-B14) 2006; 22 Beaumont (2024030523340944000_btae096-B20) 2002; 162 Hameduh (2024030523340944000_btae096-B49) 2020; 18 Tamura (2024030523340944000_btae096-B99) 2021; 38 Keane (2024030523340944000_btae096-B57) 2006; 6 Dayhoff (2024030523340944000_btae096-B33) 1978 Carvajal-Rodriguez (2024030523340944000_btae096-B25) 2006; 23 Darriba (2024030523340944000_btae096-B31) 2020; 37 Pandey (2024030523340944000_btae096-B80) 2020 Pascual-García (2024030523340944000_btae096-B81) 2019; 68 Adachi (2024030523340944000_btae096-B2) 1996; 28 Arbiza (2024030523340944000_btae096-B4) 2011; 3 Bastolla (2024030523340944000_btae096-B17) 2005; 58 Arenas (2024030523340944000_btae096-B7) 2015; 80 Branco (2024030523340944000_btae096-B24) 2022; 13 Goldstein (2024030523340944000_btae096-B45) 2013; 5 Lemmon (2024030523340944000_btae096-B65) 2004; 53 Goldstein (2024030523340944000_btae096-B44) 2011; 79 Jones (2024030523340944000_btae096-B54) 1992; 8 Nunes (2024030523340944000_btae096-B79) 2015; 7 Larson (2024030523340944000_btae096-B63) 2020; 27 Jumper (2024030523340944000_btae096-B55) 2021; 596 Woo (2024030523340944000_btae096-B104) 2014; 454–455 Robinson (2024030523340944000_btae096-B88) 2003; 20 Zhang (2024030523340944000_btae096-B110) 1999; 16 Sunnåker (2024030523340944000_btae096-B98) 2013; 9 Lopes (2024030523340944000_btae096-B68) 2014; 112 Echave (2024030523340944000_btae096-B38) 2019; 36 Arenas (2024030523340944000_btae096-B6) 2015; 6 Arenas (2024030523340944000_btae096-B8) 2022; 38 Yang (2024030523340944000_btae096-B107) 1998; 15 Waksman (2024030523340944000_btae096-B101) 1994; 236 Arenas (2024030523340944000_btae096-B11) 2015; 32 Kozlov (2024030523340944000_btae096-B61) 2019; 35 Yang (2024030523340944000_btae096-B105) 2006 Chaurasia (2024030523340944000_btae096-B26) 2022; 39 Sullivan (2024030523340944000_btae096-B97) 2005; 36 Adachi (2024030523340944000_btae096-B3) 2000; 50 Del Amparo (2024030523340944000_btae096-B36) 2023; 91 Bordner (2024030523340944000_btae096-B23) 2014; 31 Ripplinger (2024030523340944000_btae096-B87) 2010; 27 Yeh (2024030523340944000_btae096-B108) 2014; 31 Ewens (2024030523340944000_btae096-B41) 1979 Darriba (2024030523340944000_btae096-B32) 2011; 27 Kuhlman (2024030523340944000_btae096-B62) 2019; 20 Kingman (2024030523340944000_btae096-B58) 1982; 13 Csilléry (2024030523340944000_btae096-B29) 2012; 3 Minning (2024030523340944000_btae096-B71) 2013; 81 Whelan (2024030523340944000_btae096-B102) 2001; 18 Pupko (2024030523340944000_btae096-B85) 2002; 18(Suppl 1) Yu (2024030523340944000_btae096-B109) 2006; 23 Jing (2024030523340944000_btae096-B53) 2021; 1 Edgar (2024030523340944000_btae096-B40) 2004; 32 Goldstein (2024030523340944000_btae096-B46) 2017; 1 Echave (2024030523340944000_btae096-B39) 2016; 17 Thorne (2024030523340944000_btae096-B100) 2000; 10 Henikoff (2024030523340944000_btae096-B50) 1992; 89 Moshe (2024030523340944000_btae096-B73) 2022; 39 Baek (2024030523340944000_btae096-B15) 2021; 373 Nguyen (2024030523340944000_btae096-B76) 2019; 16 Yang (2024030523340944000_btae096-B106) 1994; 11 Priya (2024030523340944000_btae096-B83) 2021; 87 Neverov (2024030523340944000_btae096-B75) 2021; 17 Del Amparo (2024030523340944000_btae096-B35) 2023; 865 Sousa (2024030523340944000_btae096-B95) 2012; 108 Bastolla (2024030523340944000_btae096-B16) 2019 Zhang (2024030523340944000_btae096-B111) 1997; 44(Suppl 1) Shah (2024030523340944000_btae096-B91) 2015; 112 Arenas (2024030523340944000_btae096-B12) 2015; 32 Starr (2024030523340944000_btae096-B96) 2016; 25 Liberles (2024030523340944000_btae096-B67) 2012; 21 Wilson (2024030523340944000_btae096-B103) 2009; 26 Del Amparo (2024030523340944000_btae096-B34) 2022; 39 Grantham (2024030523340944000_btae096-B48) 1974; 185 Rawi (2024030523340944000_btae096-B86) 2015; 10 Shoemaker (2024030523340944000_btae096-B93) 1989; 6 Noivirt-Brik (2024030523340944000_btae096-B78) 2009; 5 Le (2024030523340944000_btae096-B64) 2008; 25 Beaumont (2024030523340944000_btae096-B19) 2010; 41 Luo (2024030523340944000_btae096-B69) 2010; 10 Grahnen (2024030523340944000_btae096-B47) 2012; 4 Mistry (2024030523340944000_btae096-B72) 2021; 49 Kalyaanamoorthy (2024030523340944000_btae096-B56) 2017; 14 Berezovsky (2024030523340944000_btae096-B21) 2007; 3 Bastolla (2024030523340944000_btae096-B18) 2005; 347 Ferreiro (2024030523340944000_btae096-B42) 2022; 8 Zhang (2024030523340944000_btae096-B112) 2011; 28 Puller (2024030523340944000_btae096-B84) 2020; 6 Arenas (2024030523340944000_btae096-B5) 2012; 8 Kolchanov (2024030523340944000_btae096-B59) 1983; 161 Nickle (2024030523340944000_btae096-B77) 2007; 2 Leuenberger (2024030523340944000_btae096-B66) 2010; 184 Müller (2024030523340944000_btae096-B74) 2000; 7
References_xml	– volume: 27 start-page: 1164 year: 2011 ident: 2024030523340944000_btae096-B32 article-title: ProtTest 3: fast selection of best-fit models of protein evolution publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr088 – volume: 20 start-page: 1692 year: 2003 ident: 2024030523340944000_btae096-B88 article-title: Protein evolution with dependence among codons due to tertiary structure publication-title: Mol Biol Evol doi: 10.1093/molbev/msg184 – volume: 29 start-page: 3020 year: 2013 ident: 2024030523340944000_btae096-B10 article-title: Protein evolution along phylogenetic histories under structurally constrained substitution models publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt530 – volume: 185 start-page: 862 year: 1974 ident: 2024030523340944000_btae096-B48 article-title: Amino acid difference formula to help explain protein evolution publication-title: Science doi: 10.1126/science.185.4154.862 – volume: 184 start-page: 243 year: 2010 ident: 2024030523340944000_btae096-B66 article-title: Bayesian computation and model selection without likelihoods publication-title: Genetics doi: 10.1534/genetics.109.109058 – volume: 23 start-page: 1525 year: 2006 ident: 2024030523340944000_btae096-B109 article-title: Dependence among sites in RNA evolution publication-title: Mol Biol Evol doi: 10.1093/molbev/msl015 – volume: 379 start-page: 96 year: 1996 ident: 2024030523340944000_btae096-B92 article-title: Conserved residues and the mechanism of protein folding publication-title: Nature doi: 10.1038/379096a0 – volume: 6 start-page: veaa066 year: 2020 ident: 2024030523340944000_btae096-B84 article-title: Efficient inference, potential, and limitations of site-specific substitution models publication-title: Virus Evol doi: 10.1093/ve/veaa066 – volume: 10 start-page: 99 year: 2010 ident: 2024030523340944000_btae096-B30 article-title: FLU, an amino acid substitution model for influenza proteins publication-title: BMC Evol Biol doi: 10.1186/1471-2148-10-99 – volume: 38 start-page: 3022 year: 2021 ident: 2024030523340944000_btae096-B99 article-title: MEGA11: molecular evolutionary genetics analysis version 11 publication-title: Mol Biol Evol doi: 10.1093/molbev/msab120 – volume-title: Mathematical population genetics year: 1979 ident: 2024030523340944000_btae096-B41 – volume: 102 start-page: 9541 year: 2005 ident: 2024030523340944000_btae096-B90 article-title: The application of statistical physics to evolutionary biology publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0501865102 – volume: 3 start-page: e52 year: 2007 ident: 2024030523340944000_btae096-B21 article-title: Positive and negative design in stability and thermal adaptation of natural proteins publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.0030052 – volume: 18 start-page: 3494 year: 2020 ident: 2024030523340944000_btae096-B49 article-title: Homology modeling in the time of collective and artificial intelligence publication-title: Comput Struct Biotechnol J doi: 10.1016/j.csbj.2020.11.007 – volume: 112 start-page: E3226 year: 2015 ident: 2024030523340944000_btae096-B91 article-title: Contingency and entrenchment in protein evolution under purifying selection publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1412933112 – start-page: 345 volume-title: Atlas of Protein Sequence and Structure year: 1978 ident: 2024030523340944000_btae096-B33 – volume: 27 start-page: 361 year: 2020 ident: 2024030523340944000_btae096-B63 article-title: Incorporating nearest-neighbor site dependence into protein evolution models publication-title: J Comput Biol doi: 10.1089/cmb.2019.0500 – volume: 35 start-page: 4453 year: 2019 ident: 2024030523340944000_btae096-B61 article-title: RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz305 – volume: 17 start-page: 109 year: 2016 ident: 2024030523340944000_btae096-B39 article-title: Causes of evolutionary rate variation among protein sites publication-title: Nat Rev Genet doi: 10.1038/nrg.2015.18 – volume: 18 start-page: 691 year: 2001 ident: 2024030523340944000_btae096-B102 article-title: A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach publication-title: Mol Biol Evol doi: 10.1093/oxfordjournals.molbev.a003851 – volume: 81 start-page: 1102 year: 2013 ident: 2024030523340944000_btae096-B71 article-title: Detecting selection for negative design in proteins through an improved model of the misfolded state: detecting selection for negative design publication-title: Proteins doi: 10.1002/prot.24244 – volume: 15 start-page: 1600 year: 1998 ident: 2024030523340944000_btae096-B107 article-title: Models of amino acid substitution and applications to mitochondrial protein evolution publication-title: Mol Biol Evol doi: 10.1093/oxfordjournals.molbev.a025888 – volume: 8 start-page: veac115 year: 2022 ident: 2024030523340944000_btae096-B42 article-title: The evolution of the HIV-1 protease folding stability publication-title: Virus Evol doi: 10.1093/ve/veac115 – volume: 20 start-page: 681 year: 2019 ident: 2024030523340944000_btae096-B62 article-title: Advances in protein structure prediction and design publication-title: Nat Rev Mol Cell Biol doi: 10.1038/s41580-019-0163-x – volume: 11 start-page: 316 year: 1994 ident: 2024030523340944000_btae096-B106 article-title: Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation publication-title: Mol Biol Evol – volume: 53 start-page: 265 year: 2004 ident: 2024030523340944000_btae096-B65 article-title: The importance of proper model assumption in Bayesian phylogenetics publication-title: Syst Biol doi: 10.1080/10635150490423520 – start-page: 1 year: 2020 ident: 2024030523340944000_btae096-B80 – volume: 27 start-page: 2790 year: 2010 ident: 2024030523340944000_btae096-B87 article-title: Assessment of substitution model adequacy using frequentist and bayesian methods publication-title: Mol Biol Evol doi: 10.1093/molbev/msq168 – volume: 28 start-page: 1 year: 1996 ident: 2024030523340944000_btae096-B2 article-title: Programs for molecular phylogenetics based on maximum likelihood publication-title: Comput Sci Monogr – volume: 6 start-page: 319 year: 2015 ident: 2024030523340944000_btae096-B6 article-title: Trends in substitution models of molecular evolution publication-title: Front Genet doi: 10.3389/fgene.2015.00319 – volume: 80 start-page: 189 year: 2015 ident: 2024030523340944000_btae096-B7 article-title: Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate Bayesian computation publication-title: J Mol Evol doi: 10.1007/s00239-015-9673-0 – volume: 8 start-page: 275 year: 1992 ident: 2024030523340944000_btae096-B54 article-title: The rapid generation of mutation data matrices from protein sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/8.3.275 – volume: 32 start-page: 2195 year: 2015 ident: 2024030523340944000_btae096-B12 article-title: Maximum-likelihood phylogenetic inference with selection on protein folding stability publication-title: Mol Biol Evol doi: 10.1093/molbev/msv085 – volume: 161 start-page: 65 year: 1983 ident: 2024030523340944000_btae096-B59 article-title: The effects of mutations, deletions and insertions of single amino acids on the three-dimensional structure of globins publication-title: FEBS Lett doi: 10.1016/0014-5793(83)80731-5 – volume: 10 start-page: e0143245 year: 2015 ident: 2024030523340944000_btae096-B86 article-title: Coevolution analysis of HIV-1 envelope glycoprotein complex publication-title: PLoS One doi: 10.1371/journal.pone.0143245 – volume: 39 start-page: msac231 year: 2022 ident: 2024030523340944000_btae096-B73 article-title: An approximate Bayesian computation approach for modeling genome rearrangements publication-title: Mol Biol Evol doi: 10.1093/molbev/msac231 – volume: 9 start-page: e1002803 year: 2013 ident: 2024030523340944000_btae096-B98 article-title: Approximate Bayesian computation publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1002803 – volume: 5 start-page: 1584 year: 2013 ident: 2024030523340944000_btae096-B45 article-title: Population size dependence of fitness effect distribution and substitution rate probed by biophysical model of protein thermostability publication-title: Genome Biol Evol doi: 10.1093/gbe/evt110 – volume: 13 start-page: 235 year: 1982 ident: 2024030523340944000_btae096-B58 article-title: The coalescent publication-title: Stoch Process Their Appl doi: 10.1016/0304-4149(82)90011-4 – volume: 32 start-page: 1792 year: 2004 ident: 2024030523340944000_btae096-B40 article-title: MUSCLE: multiple sequence alignment with high accuracy and high throughput publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh340 – volume: 55 start-page: 65 year: 2002 ident: 2024030523340944000_btae096-B37 article-title: rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny publication-title: J Mol Evol doi: 10.1007/s00239-001-2304-y – volume: 7 start-page: 761 year: 2000 ident: 2024030523340944000_btae096-B74 article-title: Modeling amino acid replacement publication-title: J Comput Biol doi: 10.1089/10665270050514918 – volume: 596 start-page: 583 year: 2021 ident: 2024030523340944000_btae096-B55 article-title: Highly accurate protein structure prediction with AlphaFold publication-title: Nature doi: 10.1038/s41586-021-03819-2 – volume: 347 start-page: 207 year: 2005 ident: 2024030523340944000_btae096-B89 article-title: Site interdependence attributed to tertiary structure in amino acid sequence evolution publication-title: Gene doi: 10.1016/j.gene.2004.12.011 – volume: 6 start-page: 270 year: 1989 ident: 2024030523340944000_btae096-B93 article-title: Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated publication-title: Mol Biol Evol – volume: 44(Suppl 1) start-page: S139 year: 1997 ident: 2024030523340944000_btae096-B111 article-title: Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods publication-title: J Mol Evol doi: 10.1007/PL00000067 – volume: 10 start-page: 602 year: 2000 ident: 2024030523340944000_btae096-B100 article-title: Models of protein sequence evolution and their applications publication-title: Curr Opin Genet Dev doi: 10.1016/S0959-437X(00)00142-8 – volume: 454–455 start-page: 34 year: 2014 ident: 2024030523340944000_btae096-B104 article-title: Constraints from protein structure and intra-molecular coevolution influence the fitness of HIV-1 recombinants publication-title: Virology doi: 10.1016/j.virol.2014.01.029 – volume: 16 start-page: 596 year: 2019 ident: 2024030523340944000_btae096-B76 article-title: New deep learning methods for protein loop modeling publication-title: IEEE/ACM Trans Comput Biol Bioinform doi: 10.1109/TCBB.2017.2784434 – volume: 21 start-page: 769 year: 2012 ident: 2024030523340944000_btae096-B67 article-title: The interface of protein structure, protein biophysics, and molecular evolution publication-title: Protein Sci doi: 10.1002/pro.2071 – volume-title: Computational Molecular Evolution year: 2006 ident: 2024030523340944000_btae096-B105 doi: 10.1093/acprof:oso/9780198567028.001.0001 – volume: 13 start-page: 384 year: 2022 ident: 2024030523340944000_btae096-B24 article-title: Consequences of the last glacial period on the genetic diversity of Southeast Asians publication-title: Genes (Basel) doi: 10.3390/genes13020384 – volume: 31 start-page: 135 year: 2014 ident: 2024030523340944000_btae096-B108 article-title: Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure publication-title: Mol Biol Evol doi: 10.1093/molbev/mst178 – volume: 7 start-page: 3717 year: 2017 ident: 2024030523340944000_btae096-B27 article-title: Gag-protease coevolution analyses define novel structural surfaces in the HIV-1 matrix and capsid involved in resistance to protease inhibitors publication-title: Sci Rep doi: 10.1038/s41598-017-03260-4 – volume: 66 start-page: 1054 year: 2017 ident: 2024030523340944000_btae096-B13 article-title: ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability publication-title: Syst Biol – volume: 4 start-page: 9 year: 2012 ident: 2024030523340944000_btae096-B47 article-title: CASS: protein sequence simulation with explicit genotype-phenotype mapping publication-title: Trends Evol Biol doi: 10.4081/eb.2012.e9 – volume: 68 start-page: 987 year: 2019 ident: 2024030523340944000_btae096-B81 article-title: The molecular clock in the evolution of protein structures publication-title: Syst Biol doi: 10.1093/sysbio/syz022 – volume: 52 start-page: 674 year: 2003 ident: 2024030523340944000_btae096-B70 article-title: Performance-based selection of likelihood models for phylogeny estimation publication-title: Syst Biol doi: 10.1080/10635150390235494 – volume: 32 start-page: 1109 year: 2015 ident: 2024030523340944000_btae096-B11 article-title: CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation publication-title: Mol Biol Evol doi: 10.1093/molbev/msu411 – volume: 89 start-page: 10915 year: 1992 ident: 2024030523340944000_btae096-B50 article-title: Amino acid substitution matrices from protein blocks publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.89.22.10915 – volume: 25 start-page: 1307 year: 2008 ident: 2024030523340944000_btae096-B64 article-title: An improved general amino acid replacement matrix publication-title: Mol Biol Evol doi: 10.1093/molbev/msn067 – volume: 3 start-page: 896 year: 2011 ident: 2024030523340944000_btae096-B4 article-title: Genome-wide heterogeneity of nucleotide substitution model fit publication-title: Genome Biol Evol doi: 10.1093/gbe/evr080 – volume: 39 start-page: msac144 year: 2022 ident: 2024030523340944000_btae096-B34 article-title: Consequences of substitution model selection on protein ancestral sequence reconstruction publication-title: Mol Biol Evol doi: 10.1093/molbev/msac144 – volume: 17 start-page: e1008711 year: 2021 ident: 2024030523340944000_btae096-B75 article-title: Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins publication-title: PLoS Genet doi: 10.1371/journal.pgen.1008711 – volume: 41 start-page: D344 year: 2012 ident: 2024030523340944000_btae096-B94 article-title: New and continuing developments at PROSITE publication-title: Nucleic Acids Res doi: 10.1093/nar/gks1067 – volume: 36 start-page: 613 year: 2019 ident: 2024030523340944000_btae096-B38 article-title: Beyond stability constraints: a biophysical model of enzyme evolution with selection on stability and activity publication-title: Mol Biol Evol doi: 10.1093/molbev/msy244 – volume: 6 start-page: 29 year: 2006 ident: 2024030523340944000_btae096-B57 article-title: Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified publication-title: BMC Evol Biol doi: 10.1186/1471-2148-6-29 – volume: 50 start-page: 348 year: 2000 ident: 2024030523340944000_btae096-B3 article-title: Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA publication-title: J Mol Evol doi: 10.1007/s002399910038 – volume: 37 start-page: 291 year: 2020 ident: 2024030523340944000_btae096-B31 article-title: ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models publication-title: Mol Biol Evol doi: 10.1093/molbev/msz189 – volume: 26 start-page: 2387 year: 2009 ident: 2024030523340944000_btae096-B43 article-title: Structural determinants of protein evolution are context-sensitive at the residue level publication-title: Mol Biol Evol doi: 10.1093/molbev/msp146 – volume: 112 start-page: 255 year: 2014 ident: 2024030523340944000_btae096-B68 article-title: Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation publication-title: Heredity (Edinb) doi: 10.1038/hdy.2013.101 – volume: 23 start-page: 817 year: 2006 ident: 2024030523340944000_btae096-B25 article-title: Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method publication-title: Mol. Biol. Evol doi: 10.1093/molbev/msj102 – volume: 108 start-page: 521 year: 2012 ident: 2024030523340944000_btae096-B95 article-title: Population divergence with or without admixture: selecting models using an ABC approach publication-title: Heredity (Edinb) doi: 10.1038/hdy.2011.116 – volume: 6 start-page: e5549 year: 2018 ident: 2024030523340944000_btae096-B52 article-title: Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution publication-title: PeerJ doi: 10.7717/peerj.5549 – volume: 22 start-page: 193 year: 2005 ident: 2024030523340944000_btae096-B60 article-title: Different versions of the Dayhoff rate matrix publication-title: Mol Biol Evol doi: 10.1093/molbev/msi005 – volume: 8 start-page: e1002495 year: 2012 ident: 2024030523340944000_btae096-B5 article-title: Simulation of molecular data under diverse evolutionary scenarios publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1002495 – volume: 31 start-page: 736 year: 2014 ident: 2024030523340944000_btae096-B23 article-title: A new formulation of protein evolutionary models that account for structural constraints publication-title: Mol Biol Evol doi: 10.1093/molbev/mst240 – volume: 162 start-page: 2025 year: 2002 ident: 2024030523340944000_btae096-B20 article-title: Approximate Bayesian computation in population genetics publication-title: Genetics doi: 10.1093/genetics/162.4.2025 – volume: 1 start-page: 1923 year: 2017 ident: 2024030523340944000_btae096-B46 article-title: Sequence entropy of folding and the absolute rate of amino acid substitutions publication-title: Nat Ecol Evol doi: 10.1038/s41559-017-0338-9 – start-page: 215 volume-title: Computational Methods in Protein Evolution. Vol. 1851. Methods in Molecular Biology year: 2019 ident: 2024030523340944000_btae096-B16 – volume: 41 start-page: 379 year: 2010 ident: 2024030523340944000_btae096-B19 article-title: Approximate Bayesian computation in evolution and ecology publication-title: Annu Rev Ecol Evol Syst doi: 10.1146/annurev-ecolsys-102209-144621 – volume: 49 start-page: D412 year: 2021 ident: 2024030523340944000_btae096-B72 article-title: Pfam: the protein families database in 2021 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkaa913 – volume: 36 start-page: 2086 year: 2019 ident: 2024030523340944000_btae096-B82 article-title: Modeling structural constraints on protein evolution via side-chain conformational states publication-title: Mol Biol Evol doi: 10.1093/molbev/msz122 – volume: 16 start-page: 868 year: 1999 ident: 2024030523340944000_btae096-B110 article-title: Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models publication-title: Mol Biol Evol doi: 10.1093/oxfordjournals.molbev.a026171 – volume: 13 start-page: 110 year: 2012 ident: 2024030523340944000_btae096-B51 article-title: Computer simulations: tools for population and evolutionary genetics publication-title: Nat Rev Genet doi: 10.1038/nrg3130 – volume: 58 start-page: 22 year: 2005 ident: 2024030523340944000_btae096-B17 article-title: Principal eigenvector of contact matrices and hydrophobicity profiles in proteins publication-title: Proteins doi: 10.1002/prot.20240 – volume: 347 start-page: 219 year: 2005 ident: 2024030523340944000_btae096-B18 article-title: Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles publication-title: Gene doi: 10.1016/j.gene.2004.12.015 – volume: 36 start-page: 445 year: 2005 ident: 2024030523340944000_btae096-B97 article-title: Model selection in phylogenetics publication-title: Annu Rev Ecol Evol Syst doi: 10.1146/annurev.ecolsys.36.102003.152633 – volume: 865 start-page: 147336 year: 2023 ident: 2024030523340944000_btae096-B35 article-title: Influence of substitution model selection on protein phylogenetic tree reconstruction publication-title: Gene doi: 10.1016/j.gene.2023.147336 – volume: 5 start-page: e1000592 year: 2009 ident: 2024030523340944000_btae096-B78 article-title: Trade-off between positive and negative design of protein stability: from lattice models to real proteins publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1000592 – volume: 26 start-page: 385 year: 2009 ident: 2024030523340944000_btae096-B103 article-title: Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni publication-title: Mol Biol Evol doi: 10.1093/molbev/msn264 – volume: 24 start-page: 1 year: 2007 ident: 2024030523340944000_btae096-B1 article-title: MtArt: a new model of amino acid replacement for Arthropoda publication-title: Mol Biol Evol doi: 10.1093/molbev/msl136 – volume: 14 start-page: 587 year: 2017 ident: 2024030523340944000_btae096-B56 article-title: ModelFinder: fast model selection for accurate phylogenetic estimates publication-title: Nat Methods doi: 10.1038/nmeth.4285 – volume: 7 start-page: 189 year: 2015 ident: 2024030523340944000_btae096-B79 article-title: abctools: an R package for tuning approximate Bayesian computation analyses publication-title: R Journal doi: 10.32614/RJ-2015-030 – volume: 25 start-page: 1204 year: 2016 ident: 2024030523340944000_btae096-B96 article-title: Epistasis in protein evolution publication-title: Protein Sci doi: 10.1002/pro.2897 – volume: 20 start-page: 63 year: 2010 ident: 2024030523340944000_btae096-B22 article-title: Non-linear regression models for approximate Bayesian computation publication-title: Stat Comput doi: 10.1007/s11222-009-9116-0 – volume: 236 start-page: 800 year: 1994 ident: 2024030523340944000_btae096-B101 article-title: Crystal structure of Escherichia coli thioredoxin reductase refined at 2 A resolution. Implications for a large conformational change during catalysis publication-title: J Mol Biol doi: 10.1006/jmbi.1994.1190 – volume: 22 start-page: 195 year: 2006 ident: 2024030523340944000_btae096-B14 article-title: The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti770 – volume: 28 start-page: 291 year: 2011 ident: 2024030523340944000_btae096-B112 article-title: Impact of indels on the flanking regions in structural domains publication-title: Mol Biol Evol doi: 10.1093/molbev/msq196 – volume: 1 start-page: 462 year: 2021 ident: 2024030523340944000_btae096-B53 article-title: Fast and effective protein model refinement using deep graph neural networks publication-title: Nat Comput Sci doi: 10.1038/s43588-021-00098-9 – volume: 10 start-page: 242 year: 2010 ident: 2024030523340944000_btae096-B69 article-title: Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets publication-title: BMC Evol Biol doi: 10.1186/1471-2148-10-242 – volume: 38 start-page: 58 year: 2022 ident: 2024030523340944000_btae096-B8 article-title: ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation publication-title: Bioinformatics doi: 10.1093/bioinformatics/btab617 – volume: 39 start-page: msac063 year: 2022 ident: 2024030523340944000_btae096-B26 article-title: The structural determinants of intra-protein compensatory substitutions publication-title: Mol Biol Evol doi: 10.1093/molbev/msac063 – volume: 3 start-page: 475 year: 2012 ident: 2024030523340944000_btae096-B29 article-title: abc: an R package for approximate Bayesian computation (ABC) publication-title: Methods Ecol Evol doi: 10.1111/j.2041-210X.2011.00179.x – volume: 2 start-page: e503 year: 2007 ident: 2024030523340944000_btae096-B77 article-title: HIV-specific probabilistic models of protein evolution publication-title: PLoS One doi: 10.1371/journal.pone.0000503 – volume: 91 start-page: 33 year: 2023 ident: 2024030523340944000_btae096-B36 article-title: Consequences of genetic recombination on protein folding stability publication-title: J Mol Evol doi: 10.1007/s00239-022-10080-2 – volume: 11 start-page: 248 year: 2019 ident: 2024030523340944000_btae096-B9 article-title: ProtASR2: ancestral reconstruction of protein sequences accounting for folding stability publication-title: Methods Ecol Evol doi: 10.1111/2041-210X.13341 – volume: 18(Suppl 1) start-page: S71 year: 2002 ident: 2024030523340944000_btae096-B85 article-title: Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues publication-title: Bioinformatics doi: 10.1093/bioinformatics/18.suppl_1.S71 – volume: 79 start-page: 1396 year: 2011 ident: 2024030523340944000_btae096-B44 article-title: The evolution and evolutionary consequences of marginal thermostability in proteins: evolution of protein marginal thermostability publication-title: Proteins doi: 10.1002/prot.22964 – volume: 373 start-page: 871 year: 2021 ident: 2024030523340944000_btae096-B15 article-title: Accurate prediction of protein structures and interactions using a three-track neural network publication-title: Science doi: 10.1126/science.abj8754 – volume: 68 start-page: 218 year: 2013 ident: 2024030523340944000_btae096-B28 article-title: A 20-state empirical amino-acid substitution model for green plant chloroplasts publication-title: Mol Phylogenet Evol doi: 10.1016/j.ympev.2013.03.030 – volume: 87 start-page: 104646 year: 2021 ident: 2024030523340944000_btae096-B83 article-title: Coevolutionary forces shaping the fitness of SARS-CoV-2 spike glycoprotein against human receptor ACE2 publication-title: Infect Genet Evol doi: 10.1016/j.meegid.2020.104646
SSID	ssj0005056
Score	2.4739556
Snippet	Motivation The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level,... The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level,... Motivation The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level,...
SourceID	pubmedcentral proquest pubmed crossref oup
SourceType	Open Access Repository Aggregation Database Index Database Publisher
SubjectTerms	Availability Bayes Theorem Bayesian analysis Computation Constraints Evolution Evolution, Molecular Graphical user interface Likelihood Functions Mathematical models Models, Genetic Molecular evolution Molecular modelling Original Paper Phylogeny Protein families Proteins Proteins - genetics Substitutes
Title	Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation
URI	https://www.ncbi.nlm.nih.gov/pubmed/38374231 https://www.proquest.com/docview/3213588348 https://www.proquest.com/docview/2928854728 https://pubmed.ncbi.nlm.nih.gov/PMC10914458
Volume	40
WOSCitedRecordID	wos001178651800002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
journalDatabaseRights	– providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: DOA dateStart: 20230101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1367-4811 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0005056 issn: 1367-4803 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3fa9UwFD7MsYEvzjmdV-clwp4G5bZN0pw-TnH4NAebcN9KfhUL0iv2bnjf_cM9SdvrOhDUt5akbZqcJF9ycr4P4NQUyLV2MmwvyURIbxONRZY46SQWNdpU9GIT6vISl8vyageyMRbmoQu_5AvTrAYS0UBcvDBr7Ql306ibSQyaBTeflr8PdaRRrzXwkCUCUz7GBP_xNZPpaBLidg9pPjwweW8Gujj4j7I_hScD3GTnvX0cwo5vn8F-L0C5OYKf11EGh9qGRdUhFnzJySiMu2Y9u2xg5vi6YTZAyaAo4R3raLyJhwzCo1FNp2OrmkXWh6Zl_m6waGY2LNKW_2iocJ690xsfwjaZjWoS0Syew-eLDzfvPyaDLkNiBc_XiTPCq6KWqRMqdbL0qTbcCixs5lSMUVfKaq9Mbq3nlhBJndOtJqiG1jrNX8Buu2r9S2C1LC2tkglTmEKoWpe1pUoO12lhpC5nsBibp_rW029UvducV9O6rYa6ncEZteJfZz4ZG7sa-m5X8TzjEpELnMHbbTL1uuBK0a1f3XZVXuaIUqic8hz3trH9ZFjzE0jNZoATq9lmCIze05S2-RKZvQNLqxASX_3LT7yGxzkhrXgwTpzALlmGfwN79m7ddN_n8EgtcR63Guaxr_wCbYQfdg
linkProvider	Oxford University Press
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Selection+among+site-dependent+structurally+constrained+substitution+models+of+protein+evolution+by+approximate+Bayesian+computation&rft.jtitle=Bioinformatics+%28Oxford%2C+England%29&rft.au=Ferreiro%2C+David&rft.au=Branco%2C+Catarina&rft.au=Arenas%2C+Miguel&rft.date=2024-03-04&rft.issn=1367-4811&rft.eissn=1367-4811&rft.volume=40&rft.issue=3&rft_id=info:doi/10.1093%2Fbioinformatics%2Fbtae096&rft.externalDBID=NO_FULL_TEXT
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1367-4803&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1367-4803&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1367-4803&client=summon