{"id":4665,"date":"2021-02-12T17:10:33","date_gmt":"2021-02-12T21:10:33","guid":{"rendered":"http:\/\/www2.hshsl.umaryland.edu\/hslupdates\/?p=4665"},"modified":"2021-02-12T20:51:09","modified_gmt":"2021-02-13T00:51:09","slug":"dabs-data-and-bioinformation-stuff-volume-1-issue-6-phylogenetic-trees","status":"publish","type":"post","link":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/?p=4665","title":{"rendered":"DABS (Data and Bioinformation Stuff) Volume 1 Issue 6: Phylogenetic Trees"},"content":{"rendered":"\n

The Center for Data and Bioinformation Services (CDABS) is the University of Maryland Health Sciences and Human Services Library hub for data and bioinformation learning, services, resources, and communication.<\/span>\u00a0<\/span><\/p>\n

This\u00a0<\/span>week\u00a0<\/span>(Feb 8-12) we\u00a0celebrat<\/span>ed<\/span>\u00a0Love Data Week<\/span>\u00a0and the official launch of CDABS. Check out\u00a0<\/span>our<\/span>\u00a0center, a virtual center, at our homepage:\u00a0<\/span>https:\/\/www2.hshsl.umaryland.edu\/cdabs\/<\/span><\/a>\u00a0<\/span><\/p>\n

Our topic in this edition is all<\/span>\u00a0<\/span>about phylogenetic trees! A key concept to understanding the evolution of organisms and molecules.\u00a0A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon). The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants. Two\u00a0<\/span>descendants<\/span>\u00a0that split from the same node are called sister groups.<\/span>\u00a0This\u00a0<\/span>weeks<\/span>\u00a0links will guide you to repositories of reference molecular\u00a0data to build trees as well as\u00a0<\/span>some software for building trees that is open source. Happy reading!<\/span>\u00a0<\/span><\/p>\n

    \n
  1. Berkley<\/span>\u2019s Understanding\u00a0<\/span>E<\/span>volution team is a starting point to get an overview of<\/span>\u00a0<\/span>phylogenetic<\/span>\u00a0<\/span>systematics<\/span>.\u00a0<\/span>\u00a0<\/span>In th<\/span>e<\/span>\u00a0tutorial,\u00a0<\/span>they<\/span>\u00a0<\/span>cover<\/span>\u00a0<\/span>h<\/span>ow to read an evolutionary tree,\u00a0<\/span>h<\/span>ow to classify organisms based on evolutionary trees,\u00a0<\/span>h<\/span>ow to reconstruct an evolutionary tree,\u00a0<\/span>and h<\/span>ow evolutionary trees are\u00a0<\/span>used.<\/span> (5\u2013minute read) <\/span>https:\/\/evolution.berkeley.edu\/evolibrary\/article\/0_0_0\/phylogenetics_01<\/span><\/a>\u00a0<\/span><\/li>\n
  2. Find<\/span>ing<\/span>\u00a0high quality<\/span>,<\/span>\u00a0reliable data is fundamental to building phylogenetic trees that are reliable.\u00a0<\/span>GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. The knowledgebase automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.<\/span>\u00a0(<\/span>5-minute<\/span>\u00a0overview & Infinite time exploring)<\/span> \u00a0<\/span>https:\/\/www.genecards.org\/<\/span><\/a>\u00a0<\/span><\/li>\n
  3. To build a molecular phylogenetic tree you will need to run a multiple sequence alignment<\/span><\/span>\u00a0and use the phylogenetic tree output<\/span><\/span>. One of the fundamental molecular biology tools for doing so<\/span><\/span>\u00a0is\u00a0<\/span><\/span>Clustal<\/span><\/span>\u00a0Omega\u00a0“The last alignment program you’ll ever need”.\u00a0<\/span><\/span>Clustal<\/span><\/span>\u00a0Omega can be downloaded and run on your computer or you can also access a webserver to perform your\u00a0<\/span><\/span>alignment. (5-minute overview)<\/span><\/span>\u00a0<\/span>http:\/\/www.clustal.org\/omega\/<\/a> \u00a0<\/li>\n
  4. Evolview<\/span>\u00a0is an interactive tree visualization tool designed to help researchers in visualizing phylogenetic trees and in annotating these with additional information. It offers the user with a platform to upload trees in most common tree formats, such as\u00a0<\/span>Newick<\/span>\/<\/span>Phylip<\/span>, Nexus,\u00a0<\/span>Nhx<\/span>\u00a0and\u00a0<\/span>PhyloXML<\/span>, and provides a range of visualization options, using fifteen types of custom annotation datasets.<\/span> (5-minute overview) <\/span><\/span><\/span>www.evolgenius.info\/evolview\/<\/span><\/a>\u00a0<\/span><\/li>\n
  5. Cytoscape<\/span>\u00a0is an\u00a0<\/span>open source<\/span>\u00a0software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. In\u00a0<\/span>addition<\/span> it is a tool for building phylogenetic trees. (5-minute overview)<\/span><\/span> <\/span>https:\/\/cytoscape.org<\/span><\/a>\u00a0<\/span><\/li>\n
  6. There is an R package<\/span>\u00a0RCy3<\/span>\u00a0that can be leveraged for creating\u00a0<\/span>phylogenetic trees in R and visualizing them in\u00a0<\/span>Cytoscape<\/span>.\u00a0This vignette will show you how to work the popular\u00a0<\/span>Newick<\/span>\u00a0format for phylogenetic trees in\u00a0<\/span>Cytoscape<\/span>\u00a0by conversion to\u00a0<\/span>igraph<\/span> and import via RCy3. (5-minute overview)<\/span><\/span><\/span> http:\/\/cytoscape.org\/cytoscape-automation\/for-scripters\/R\/notebooks\/Phylogenetic-trees.nb.html<\/span><\/a>\u00a0<\/span><\/li>\n<\/ol>\n

    Questions?\u00a0<\/span><\/b>\u00a0<\/span><\/p>\n

    Contact:\u00a0<\/span><\/b>Amy Yarnell<\/span><\/b>, Data Services Librarian and\u00a0<\/span>Jean-Paul Courneya<\/span><\/b>,\u00a0Bioinformationist\u00a0— at<\/span>\u202f<\/span>data@hshsl.umaryland.edu<\/span><\/a>.<\/span>\u00a0<\/span><\/p>\n

      \n
    1. \u00a0<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

      The Center for Data and Bioinformation Services (CDABS) is the University of Maryland Health Sciences and Human Services Library hub for data and bioinformation learning, services, resources, and communication.\u00a0 This\u00a0week\u00a0(Feb 8-12) we\u00a0celebrated\u00a0Love Data Week\u00a0and the official launch of CDABS. Check … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[290],"tags":[65,270,269,271,314,315],"class_list":["post-4665","post","type-post","status-publish","format-standard","hentry","category-data-bioinformation","tag-bioinformatics","tag-bioinformation","tag-cdabs","tag-data","tag-evolution","tag-phylogenetics"],"_links":{"self":[{"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=\/wp\/v2\/posts\/4665"}],"collection":[{"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=4665"}],"version-history":[{"count":6,"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=\/wp\/v2\/posts\/4665\/revisions"}],"predecessor-version":[{"id":4712,"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=\/wp\/v2\/posts\/4665\/revisions\/4712"}],"wp:attachment":[{"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4665"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4665"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www2.hshsl.umaryland.edu\/hslupdates\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4665"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}