GenPhyloData: realistic simulation of gene family evolution
PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known...
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| Veröffentlicht in: | BMC bioinformatics 2013-06, Vol.14 (1), p.209-209, Article 209 |
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| creator | Sjöstrand, Joel Arvestad, Lars Lagergren, Jens Sennblad, Bengt |
| description | PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock.
Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data.
The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution. |
| doi_str_mv | 10.1186/1471-2105-14-209 |
| format | Article |
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Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data.
The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.</description><identifier>ISSN: 1471-2105</identifier><identifier>EISSN: 1471-2105</identifier><identifier>DOI: 10.1186/1471-2105-14-209</identifier><identifier>PMID: 23803001</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Accounting ; Applications software ; Biogeography ; Bioinformatics ; Biological ; Biological Clocks - genetics ; Bulk molding compounds ; Computer Simulation ; Evolution ; Evolution, Molecular ; Gene duplication ; Gene Duplication - genetics ; Gene family ; Gene loss ; Gene Transfer Techniques ; Genes ; Host-parasite co-evolution ; Humans ; LGT ; Models, Biological ; Molecular clock ; Multigene Family - genetics ; Phylogenetic trees ; Phylogenetics ; Phylogeny ; Physiological aspects ; Simulation ; Software ; Species Specificity ; Synthetic data ; Trees</subject><ispartof>BMC bioinformatics, 2013-06, Vol.14 (1), p.209-209, Article 209</ispartof><rights>COPYRIGHT 2013 BioMed Central Ltd.</rights><rights>Copyright © 2013 Sjöstrand et al.; licensee BioMed Central Ltd. 2013 Sjöstrand et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b662t-54e41d0d2ac0cb5ebefc8a1a22084e8a4ff4d88a9272a3b3ded7fec43ccee7433</citedby><cites>FETCH-LOGICAL-b662t-54e41d0d2ac0cb5ebefc8a1a22084e8a4ff4d88a9272a3b3ded7fec43ccee7433</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703295/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703295/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,550,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23803001$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-124972$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-92509$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:126891317$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Sjöstrand, Joel</creatorcontrib><creatorcontrib>Arvestad, Lars</creatorcontrib><creatorcontrib>Lagergren, Jens</creatorcontrib><creatorcontrib>Sennblad, Bengt</creatorcontrib><title>GenPhyloData: realistic simulation of gene family evolution</title><title>BMC bioinformatics</title><addtitle>BMC Bioinformatics</addtitle><description>PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock.
Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data.
The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.</description><subject>Accounting</subject><subject>Applications software</subject><subject>Biogeography</subject><subject>Bioinformatics</subject><subject>Biological</subject><subject>Biological Clocks - genetics</subject><subject>Bulk molding compounds</subject><subject>Computer Simulation</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Gene duplication</subject><subject>Gene Duplication - genetics</subject><subject>Gene family</subject><subject>Gene loss</subject><subject>Gene Transfer Techniques</subject><subject>Genes</subject><subject>Host-parasite co-evolution</subject><subject>Humans</subject><subject>LGT</subject><subject>Models, Biological</subject><subject>Molecular clock</subject><subject>Multigene Family - genetics</subject><subject>Phylogenetic trees</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Simulation</subject><subject>Software</subject><subject>Species Specificity</subject><subject>Synthetic data</subject><subject>Trees</subject><issn>1471-2105</issn><issn>1471-2105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>D8T</sourceid><recordid>eNqFkk1v1DAQhiNERT_gzglF4oJUhXr8ETsgIa220FaqBAfgajnOZNfUids4Kdp_T0KWVVeicPJ45plXr2YmSV4CeQug8jPgEjIKRGTAM0qKJ8nRLvX0QXyYHMf4gxCQiohnySFlirDxe5S8v8D2y3rjw7npzbu0Q-Nd7J1No2sGb3oX2jTU6QpbTGvTOL9J8T74YSo8Tw5q4yO-2L4nybdPH78uL7PrzxdXy8V1VuY57TPBkUNFKmossaXAEmurDBhKieKoDK9rXillCiqpYSWrsJI1Ws6sRZScsZMkm3XjT7wdSn3bucZ0Gx2M09vUzRihFlQJBSN_-ih_7r4vdOhWOg66oIIU_1Tf0Tf9WgPlhaQj_2HmR7jBymLbd8bvte1XWrfWq3CvmSSMFmIUWM4CpQuPCOxXbGj0tEo9rXKMNP1t-83WRhfuBoy9bly06L1pMQxRQy6B55xw8X-UAxUgC8hH9PWMroxH7do6jA7shOuFYFyAEGJaCJkp24UYO6x35oHo6TD_ZvfVw6ntGv5cIvsF8cffYQ</recordid><startdate>20130627</startdate><enddate>20130627</enddate><creator>Sjöstrand, Joel</creator><creator>Arvestad, Lars</creator><creator>Lagergren, Jens</creator><creator>Sennblad, Bengt</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7SC</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>D8V</scope><scope>ABAVF</scope><scope>D8T</scope><scope>DG7</scope><scope>ZZAVC</scope></search><sort><creationdate>20130627</creationdate><title>GenPhyloData: realistic simulation of gene family evolution</title><author>Sjöstrand, Joel ; Arvestad, Lars ; Lagergren, Jens ; Sennblad, Bengt</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b662t-54e41d0d2ac0cb5ebefc8a1a22084e8a4ff4d88a9272a3b3ded7fec43ccee7433</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Accounting</topic><topic>Applications software</topic><topic>Biogeography</topic><topic>Bioinformatics</topic><topic>Biological</topic><topic>Biological Clocks - genetics</topic><topic>Bulk molding compounds</topic><topic>Computer Simulation</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Gene duplication</topic><topic>Gene Duplication - genetics</topic><topic>Gene family</topic><topic>Gene loss</topic><topic>Gene Transfer Techniques</topic><topic>Genes</topic><topic>Host-parasite co-evolution</topic><topic>Humans</topic><topic>LGT</topic><topic>Models, Biological</topic><topic>Molecular clock</topic><topic>Multigene Family - genetics</topic><topic>Phylogenetic trees</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Physiological aspects</topic><topic>Simulation</topic><topic>Software</topic><topic>Species Specificity</topic><topic>Synthetic data</topic><topic>Trees</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sjöstrand, Joel</creatorcontrib><creatorcontrib>Arvestad, Lars</creatorcontrib><creatorcontrib>Lagergren, Jens</creatorcontrib><creatorcontrib>Sennblad, Bengt</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Kungliga Tekniska Högskolan</collection><collection>SWEPUB Stockholms universitet full text</collection><collection>SWEPUB Freely available online</collection><collection>SWEPUB Stockholms universitet</collection><collection>SwePub Articles full text</collection><jtitle>BMC bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sjöstrand, Joel</au><au>Arvestad, Lars</au><au>Lagergren, Jens</au><au>Sennblad, Bengt</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>GenPhyloData: realistic simulation of gene family evolution</atitle><jtitle>BMC bioinformatics</jtitle><addtitle>BMC Bioinformatics</addtitle><date>2013-06-27</date><risdate>2013</risdate><volume>14</volume><issue>1</issue><spage>209</spage><epage>209</epage><pages>209-209</pages><artnum>209</artnum><issn>1471-2105</issn><eissn>1471-2105</eissn><abstract>PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. 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Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data.
The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>23803001</pmid><doi>10.1186/1471-2105-14-209</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Springer Nature - Complete Springer Journals; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; SWEPUB Freely available online; PubMed Central Open Access; Springer Nature OA Free Journals |
| subjects | Accounting Applications software Biogeography Bioinformatics Biological Biological Clocks - genetics Bulk molding compounds Computer Simulation Evolution Evolution, Molecular Gene duplication Gene Duplication - genetics Gene family Gene loss Gene Transfer Techniques Genes Host-parasite co-evolution Humans LGT Models, Biological Molecular clock Multigene Family - genetics Phylogenetic trees Phylogenetics Phylogeny Physiological aspects Simulation Software Species Specificity Synthetic data Trees |
| title | GenPhyloData: realistic simulation of gene family evolution |
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