Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Abstract Motivation Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software, from host/symbiont to species/gene comparisons) is av...
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| Veröffentlicht in: | Bioinformatics 2022-04, Vol.38 (8), p.2350-2352 |
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| container_title | Bioinformatics |
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| creator | Penel, Simon Menet, Hugo Tricou, Théo Daubin, Vincent Tannier, Eric |
| description | Abstract
Motivation
Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software, from host/symbiont to species/gene comparisons) is available to visualize reconciliation results. Moreover there is no tool to visualize 3-levels reconciliations, i.e. to visualize 2 nested reconciliations as for example in a host/symbiont/gene complex.
Results
Thirdkind is a light and easy to install command line software producing svg files displaying reconciliations, including 3-levels reconciliations. It takes a standard format recPhyloXML as input, and is thus usable with most reconciliation software.
Availability and implementation
https://github.com/simonpenel/thirdkind/wiki.
Supplementary information
Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btac062 |
| format | Article |
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Motivation
Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software, from host/symbiont to species/gene comparisons) is available to visualize reconciliation results. Moreover there is no tool to visualize 3-levels reconciliations, i.e. to visualize 2 nested reconciliations as for example in a host/symbiont/gene complex.
Results
Thirdkind is a light and easy to install command line software producing svg files displaying reconciliations, including 3-levels reconciliations. It takes a standard format recPhyloXML as input, and is thus usable with most reconciliation software.
Availability and implementation
https://github.com/simonpenel/thirdkind/wiki.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btac062</identifier><identifier>PMID: 35139153</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Bioinformatics ; Computer Science ; Phylogeny ; Software</subject><ispartof>Bioinformatics, 2022-04, Vol.38 (8), p.2350-2352</ispartof><rights>The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2022</rights><rights>The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c435t-120ce39ac75dd92ad3689d2c67a1d268ede0b0b0e65ac854c587c7541c83a0223</citedby><cites>FETCH-LOGICAL-c435t-120ce39ac75dd92ad3689d2c67a1d268ede0b0b0e65ac854c587c7541c83a0223</cites><orcidid>0000-0003-1550-5477 ; 0000-0002-4432-2680 ; 0000-0001-8269-9430 ; 0000-0002-3681-7536</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,1604,27924,27925</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btac062$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35139153$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-03563666$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Schwartz, Russell</contributor><creatorcontrib>Penel, Simon</creatorcontrib><creatorcontrib>Menet, Hugo</creatorcontrib><creatorcontrib>Tricou, Théo</creatorcontrib><creatorcontrib>Daubin, Vincent</creatorcontrib><creatorcontrib>Tannier, Eric</creatorcontrib><title>Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software, from host/symbiont to species/gene comparisons) is available to visualize reconciliation results. Moreover there is no tool to visualize 3-levels reconciliations, i.e. to visualize 2 nested reconciliations as for example in a host/symbiont/gene complex.
Results
Thirdkind is a light and easy to install command line software producing svg files displaying reconciliations, including 3-levels reconciliations. It takes a standard format recPhyloXML as input, and is thus usable with most reconciliation software.
Availability and implementation
https://github.com/simonpenel/thirdkind/wiki.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><subject>Bioinformatics</subject><subject>Computer Science</subject><subject>Phylogeny</subject><subject>Software</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkMtKBDEQRYMovn9BeqmL1ry7252ILxxwo-uQTmqcaCZpk25h_t7IjII7qUUVxbm3iovQCcHnBHfsonfRhXlMSz06ky_6URss6RbaJ1zimmLRbZeZyabmLWZ76CDnN4wF4Zzvoj0mCOuIYPvo8Xnhkn13wV5W1uXB65ULr9WwWPn4CgGKewXBxCmMkHLVwyoGW9Hawyf4KoGJwTjvyhcxHKGdufYZjjf9EL3c3jxf39ezp7uH66tZbTgTY00oNsA6bRphbUe1ZbLtLDWy0cRS2YIF3JcCKbRpBTeibQrLiWmZxpSyQ3S29l1or4bkljqtVNRO3V_N1PcOMyGZlPKTFPZ0zQ4pfkyQR7V02YD3OkCcsqKSNrxlQnQFlWvUpJhzgvmvN8HqO3T1N3S1Cb0ITzY3pn4J9lf2k3IByBqI0_Bf0y-6l5UW</recordid><startdate>20220412</startdate><enddate>20220412</enddate><creator>Penel, Simon</creator><creator>Menet, Hugo</creator><creator>Tricou, Théo</creator><creator>Daubin, Vincent</creator><creator>Tannier, Eric</creator><general>Oxford University Press</general><general>Oxford University Press (OUP)</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>1XC</scope><scope>VOOES</scope><orcidid>https://orcid.org/0000-0003-1550-5477</orcidid><orcidid>https://orcid.org/0000-0002-4432-2680</orcidid><orcidid>https://orcid.org/0000-0001-8269-9430</orcidid><orcidid>https://orcid.org/0000-0002-3681-7536</orcidid></search><sort><creationdate>20220412</creationdate><title>Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation</title><author>Penel, Simon ; Menet, Hugo ; Tricou, Théo ; Daubin, Vincent ; Tannier, Eric</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c435t-120ce39ac75dd92ad3689d2c67a1d268ede0b0b0e65ac854c587c7541c83a0223</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Bioinformatics</topic><topic>Computer Science</topic><topic>Phylogeny</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Penel, Simon</creatorcontrib><creatorcontrib>Menet, Hugo</creatorcontrib><creatorcontrib>Tricou, Théo</creatorcontrib><creatorcontrib>Daubin, Vincent</creatorcontrib><creatorcontrib>Tannier, Eric</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>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Penel, Simon</au><au>Menet, Hugo</au><au>Tricou, Théo</au><au>Daubin, Vincent</au><au>Tannier, Eric</au><au>Schwartz, Russell</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2022-04-12</date><risdate>2022</risdate><volume>38</volume><issue>8</issue><spage>2350</spage><epage>2352</epage><pages>2350-2352</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software, from host/symbiont to species/gene comparisons) is available to visualize reconciliation results. Moreover there is no tool to visualize 3-levels reconciliations, i.e. to visualize 2 nested reconciliations as for example in a host/symbiont/gene complex.
Results
Thirdkind is a light and easy to install command line software producing svg files displaying reconciliations, including 3-levels reconciliations. It takes a standard format recPhyloXML as input, and is thus usable with most reconciliation software.
Availability and implementation
https://github.com/simonpenel/thirdkind/wiki.
Supplementary information
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>35139153</pmid><doi>10.1093/bioinformatics/btac062</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0003-1550-5477</orcidid><orcidid>https://orcid.org/0000-0002-4432-2680</orcidid><orcidid>https://orcid.org/0000-0001-8269-9430</orcidid><orcidid>https://orcid.org/0000-0002-3681-7536</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Bioinformatics, 2022-04, Vol.38 (8), p.2350-2352 |
| issn | 1367-4803 1460-2059 1367-4811 |
| language | eng |
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| source | Oxford Journals Open Access Collection |
| subjects | Bioinformatics Computer Science Phylogeny Software |
| title | Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation |
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