PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context
Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread...
Gespeichert in:
| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2017-12, Vol.33 (24), p.3993-3995 |
|---|---|
| Hauptverfasser: | , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 3995 |
|---|---|
| container_issue | 24 |
| container_start_page | 3993 |
| container_title | Bioinformatics (Oxford, England) |
| container_volume | 33 |
| creator | Libin, Pieter Vanden Eynden, Ewout Incardona, Francesca Nowé, Ann Bezenchek, Antonia Sönnerborg, Anders Vandamme, Anne-Mieke Theys, Kristof Baele, Guy |
| description | Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially encompassing tens of thousands of virus strains, an efficient method for data exploration is required. The clades that are visited during this exploration should be annotated with strain characteristics (e.g. transmission risk group, tropism, drug resistance profile) and their geographic context.
PhyloGeoTool implements a visual method to explore large phylogenetic trees and to depict characteristics of strains and clades, including their geographic context, in an interactive way. PhyloGeoTool also provides the possibility to position new virus strains relative to the existing phylogenetic tree, allowing users to gain insight in the placement of such new strains without the need to perform a de novo reconstruction of the phylogeny.
https://github.com/rega-cev/phylogeotool (Freely available: open source software project).
phylogeotool@kuleuven.be.
Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btx535 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_swepu</sourceid><recordid>TN_cdi_swepub_primary_oai_swepub_ki_se_493721</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1945214882</sourcerecordid><originalsourceid>FETCH-LOGICAL-c499t-30d8482060f538603b6b31c058aa29dd6c94102ca30b23c86d8c8e724e50f5fb3</originalsourceid><addsrcrecordid>eNp1kc1O3DAUha0KVP76CEVZsgn4f-wukBBqaSUkWMDacpybwa0Tp3aGzrx9jWYYmAUrX9nfd2zrIPSV4HOCNbtofPRDF1NvJ-_yRTMtBROf0CFhclZzRcjedsbsAB3l_BtjLLCQn9EBVVoSTdkherx_WoV4A_EhxvCt8sMEybrJP0NYVbAcQ0x-mFfBpjlU4ws7h8FDLmRlhwpG30LvY9n2zobKxRKwnE7QfmdDhi-b9Rg9_vj-cP2zvr27-XV9dVs7rvVUM9wqriiWuBNMScwa2TDisFDWUt220mlOMHWW4YYyp2SrnIIZ5SCK0TXsGNXr3PwPxkVjxuR7m1YmWm82W3_KBIZrNqOk8PpDfkyxfZNeRVI8LgkXxb1cuwXooXUwTMmG3Yidk8E_mXl8NqL8DGteAs42ASn-XUCeTO-zgxDsAHGRDdFcUMKVogUVa9SlmHOCbnsNwealfrNbv1nXX7zT92_cWq99s__smLWn</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1945214882</pqid></control><display><type>article</type><title>PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context</title><source>MEDLINE</source><source>Access via Oxford University Press (Open Access Collection)</source><source>SWEPUB Freely available online</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Alma/SFX Local Collection</source><creator>Libin, Pieter ; Vanden Eynden, Ewout ; Incardona, Francesca ; Nowé, Ann ; Bezenchek, Antonia ; Sönnerborg, Anders ; Vandamme, Anne-Mieke ; Theys, Kristof ; Baele, Guy</creator><contributor>Kelso, Janet</contributor><creatorcontrib>Libin, Pieter ; Vanden Eynden, Ewout ; Incardona, Francesca ; Nowé, Ann ; Bezenchek, Antonia ; Sönnerborg, Anders ; Vandamme, Anne-Mieke ; Theys, Kristof ; Baele, Guy ; EucoHIV Study Group ; EucoHIV Study Group ; Kelso, Janet</creatorcontrib><description>Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially encompassing tens of thousands of virus strains, an efficient method for data exploration is required. The clades that are visited during this exploration should be annotated with strain characteristics (e.g. transmission risk group, tropism, drug resistance profile) and their geographic context.
PhyloGeoTool implements a visual method to explore large phylogenetic trees and to depict characteristics of strains and clades, including their geographic context, in an interactive way. PhyloGeoTool also provides the possibility to position new virus strains relative to the existing phylogenetic tree, allowing users to gain insight in the placement of such new strains without the need to perform a de novo reconstruction of the phylogeny.
https://github.com/rega-cev/phylogeotool (Freely available: open source software project).
phylogeotool@kuleuven.be.
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>ISSN: 1367-4811</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btx535</identifier><identifier>PMID: 28961923</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Notes ; Bioinformatik (beräkningsbiologi) (tillämpningar under 10610) ; Cluster Analysis ; Computational Biology - methods ; Data- och informationsvetenskap (Datateknik) ; Databases, Nucleic Acid ; Epidemiologic Methods ; Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi ; Humans ; Hälsovetenskap ; Medicin och hälsovetenskap ; Naturvetenskap ; Phylogeny ; Software ; Virus Diseases - epidemiology</subject><ispartof>Bioinformatics (Oxford, England), 2017-12, Vol.33 (24), p.3993-3995</ispartof><rights>The Author(s) 2017. Published by Oxford University Press.</rights><rights>The Author 2017. Published by Oxford University Press. 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c499t-30d8482060f538603b6b31c058aa29dd6c94102ca30b23c86d8c8e724e50f5fb3</citedby><cites>FETCH-LOGICAL-c499t-30d8482060f538603b6b31c058aa29dd6c94102ca30b23c86d8c8e724e50f5fb3</cites><orcidid>0000-0003-3906-758X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860094/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860094/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,553,728,781,785,886,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28961923$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:137246145$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><contributor>Kelso, Janet</contributor><creatorcontrib>Libin, Pieter</creatorcontrib><creatorcontrib>Vanden Eynden, Ewout</creatorcontrib><creatorcontrib>Incardona, Francesca</creatorcontrib><creatorcontrib>Nowé, Ann</creatorcontrib><creatorcontrib>Bezenchek, Antonia</creatorcontrib><creatorcontrib>Sönnerborg, Anders</creatorcontrib><creatorcontrib>Vandamme, Anne-Mieke</creatorcontrib><creatorcontrib>Theys, Kristof</creatorcontrib><creatorcontrib>Baele, Guy</creatorcontrib><creatorcontrib>EucoHIV Study Group</creatorcontrib><creatorcontrib>EucoHIV Study Group</creatorcontrib><title>PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context</title><title>Bioinformatics (Oxford, England)</title><addtitle>Bioinformatics</addtitle><description>Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially encompassing tens of thousands of virus strains, an efficient method for data exploration is required. The clades that are visited during this exploration should be annotated with strain characteristics (e.g. transmission risk group, tropism, drug resistance profile) and their geographic context.
PhyloGeoTool implements a visual method to explore large phylogenetic trees and to depict characteristics of strains and clades, including their geographic context, in an interactive way. PhyloGeoTool also provides the possibility to position new virus strains relative to the existing phylogenetic tree, allowing users to gain insight in the placement of such new strains without the need to perform a de novo reconstruction of the phylogeny.
https://github.com/rega-cev/phylogeotool (Freely available: open source software project).
phylogeotool@kuleuven.be.
Supplementary data are available at Bioinformatics online.</description><subject>Applications Notes</subject><subject>Bioinformatik (beräkningsbiologi) (tillämpningar under 10610)</subject><subject>Cluster Analysis</subject><subject>Computational Biology - methods</subject><subject>Data- och informationsvetenskap (Datateknik)</subject><subject>Databases, Nucleic Acid</subject><subject>Epidemiologic Methods</subject><subject>Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi</subject><subject>Humans</subject><subject>Hälsovetenskap</subject><subject>Medicin och hälsovetenskap</subject><subject>Naturvetenskap</subject><subject>Phylogeny</subject><subject>Software</subject><subject>Virus Diseases - epidemiology</subject><issn>1367-4803</issn><issn>1367-4811</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>D8T</sourceid><recordid>eNp1kc1O3DAUha0KVP76CEVZsgn4f-wukBBqaSUkWMDacpybwa0Tp3aGzrx9jWYYmAUrX9nfd2zrIPSV4HOCNbtofPRDF1NvJ-_yRTMtBROf0CFhclZzRcjedsbsAB3l_BtjLLCQn9EBVVoSTdkherx_WoV4A_EhxvCt8sMEybrJP0NYVbAcQ0x-mFfBpjlU4ws7h8FDLmRlhwpG30LvY9n2zobKxRKwnE7QfmdDhi-b9Rg9_vj-cP2zvr27-XV9dVs7rvVUM9wqriiWuBNMScwa2TDisFDWUt220mlOMHWW4YYyp2SrnIIZ5SCK0TXsGNXr3PwPxkVjxuR7m1YmWm82W3_KBIZrNqOk8PpDfkyxfZNeRVI8LgkXxb1cuwXooXUwTMmG3Yidk8E_mXl8NqL8DGteAs42ASn-XUCeTO-zgxDsAHGRDdFcUMKVogUVa9SlmHOCbnsNwealfrNbv1nXX7zT92_cWq99s__smLWn</recordid><startdate>20171215</startdate><enddate>20171215</enddate><creator>Libin, Pieter</creator><creator>Vanden Eynden, Ewout</creator><creator>Incardona, Francesca</creator><creator>Nowé, Ann</creator><creator>Bezenchek, Antonia</creator><creator>Sönnerborg, Anders</creator><creator>Vandamme, Anne-Mieke</creator><creator>Theys, Kristof</creator><creator>Baele, Guy</creator><general>Oxford University Press</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>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>D8T</scope><scope>ZZAVC</scope><orcidid>https://orcid.org/0000-0003-3906-758X</orcidid></search><sort><creationdate>20171215</creationdate><title>PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context</title><author>Libin, Pieter ; Vanden Eynden, Ewout ; Incardona, Francesca ; Nowé, Ann ; Bezenchek, Antonia ; Sönnerborg, Anders ; Vandamme, Anne-Mieke ; Theys, Kristof ; Baele, Guy</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c499t-30d8482060f538603b6b31c058aa29dd6c94102ca30b23c86d8c8e724e50f5fb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Applications Notes</topic><topic>Bioinformatik (beräkningsbiologi) (tillämpningar under 10610)</topic><topic>Cluster Analysis</topic><topic>Computational Biology - methods</topic><topic>Data- och informationsvetenskap (Datateknik)</topic><topic>Databases, Nucleic Acid</topic><topic>Epidemiologic Methods</topic><topic>Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi</topic><topic>Humans</topic><topic>Hälsovetenskap</topic><topic>Medicin och hälsovetenskap</topic><topic>Naturvetenskap</topic><topic>Phylogeny</topic><topic>Software</topic><topic>Virus Diseases - epidemiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Libin, Pieter</creatorcontrib><creatorcontrib>Vanden Eynden, Ewout</creatorcontrib><creatorcontrib>Incardona, Francesca</creatorcontrib><creatorcontrib>Nowé, Ann</creatorcontrib><creatorcontrib>Bezenchek, Antonia</creatorcontrib><creatorcontrib>Sönnerborg, Anders</creatorcontrib><creatorcontrib>Vandamme, Anne-Mieke</creatorcontrib><creatorcontrib>Theys, Kristof</creatorcontrib><creatorcontrib>Baele, Guy</creatorcontrib><creatorcontrib>EucoHIV Study Group</creatorcontrib><creatorcontrib>EucoHIV Study Group</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Freely available online</collection><collection>SwePub Articles full text</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Libin, Pieter</au><au>Vanden Eynden, Ewout</au><au>Incardona, Francesca</au><au>Nowé, Ann</au><au>Bezenchek, Antonia</au><au>Sönnerborg, Anders</au><au>Vandamme, Anne-Mieke</au><au>Theys, Kristof</au><au>Baele, Guy</au><au>Kelso, Janet</au><aucorp>EucoHIV Study Group</aucorp><aucorp>EucoHIV Study Group</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><addtitle>Bioinformatics</addtitle><date>2017-12-15</date><risdate>2017</risdate><volume>33</volume><issue>24</issue><spage>3993</spage><epage>3995</epage><pages>3993-3995</pages><issn>1367-4803</issn><issn>1367-4811</issn><eissn>1367-4811</eissn><abstract>Clinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially encompassing tens of thousands of virus strains, an efficient method for data exploration is required. The clades that are visited during this exploration should be annotated with strain characteristics (e.g. transmission risk group, tropism, drug resistance profile) and their geographic context.
PhyloGeoTool implements a visual method to explore large phylogenetic trees and to depict characteristics of strains and clades, including their geographic context, in an interactive way. PhyloGeoTool also provides the possibility to position new virus strains relative to the existing phylogenetic tree, allowing users to gain insight in the placement of such new strains without the need to perform a de novo reconstruction of the phylogeny.
https://github.com/rega-cev/phylogeotool (Freely available: open source software project).
phylogeotool@kuleuven.be.
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>28961923</pmid><doi>10.1093/bioinformatics/btx535</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0003-3906-758X</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1367-4803 |
| ispartof | Bioinformatics (Oxford, England), 2017-12, Vol.33 (24), p.3993-3995 |
| issn | 1367-4803 1367-4811 1367-4811 |
| language | eng |
| recordid | cdi_swepub_primary_oai_swepub_ki_se_493721 |
| source | MEDLINE; Access via Oxford University Press (Open Access Collection); SWEPUB Freely available online; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Applications Notes Bioinformatik (beräkningsbiologi) (tillämpningar under 10610) Cluster Analysis Computational Biology - methods Data- och informationsvetenskap (Datateknik) Databases, Nucleic Acid Epidemiologic Methods Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi Humans Hälsovetenskap Medicin och hälsovetenskap Naturvetenskap Phylogeny Software Virus Diseases - epidemiology |
| title | PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-12T03%3A32%3A05IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_swepu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=PhyloGeoTool:%20interactively%20exploring%20large%20phylogenies%20in%20an%20epidemiological%20context&rft.jtitle=Bioinformatics%20(Oxford,%20England)&rft.au=Libin,%20Pieter&rft.aucorp=EucoHIV%20Study%20Group&rft.date=2017-12-15&rft.volume=33&rft.issue=24&rft.spage=3993&rft.epage=3995&rft.pages=3993-3995&rft.issn=1367-4803&rft.eissn=1367-4811&rft_id=info:doi/10.1093/bioinformatics/btx535&rft_dat=%3Cproquest_swepu%3E1945214882%3C/proquest_swepu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1945214882&rft_id=info:pmid/28961923&rfr_iscdi=true |