{"id":36137,"date":"2023-07-06T09:50:01","date_gmt":"2023-07-06T09:50:01","guid":{"rendered":"https:\/\/www.embl.org\/ells\/?post_type=teachingbase&#038;p=36137"},"modified":"2023-07-14T07:23:16","modified_gmt":"2023-07-14T07:23:16","slug":"part-4-phylogenetic-analysis","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/part-4-phylogenetic-analysis\/","title":{"rendered":"Part 4: Phylogenetic analysis"},"content":{"rendered":"\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-642f7ed5-2993-4c31-b70b-7ffd8ff9c04d\" data-vf-js-location-nearest-activation-target=\"\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-1eaf137f-ffdd-46e0-beee-42834893e5ab\" data-vf-js-location-nearest-activation-target=\"\">Your task<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-69241370-32fb-4b41-bb67-bfbd37b87933\" data-vf-js-location-nearest-activation-target=\"\">Simple Phylogeny<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-00d9f095-46a3-40b6-84e5-e898498f61b3\" data-vf-js-location-nearest-activation-target=\"\">Questions<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-5b32989c-1503-4b3e-90ed-b4adf182864e\" data-vf-js-location-nearest-activation-target=\"\">Activity navigation<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-642f7ed5-2993-4c31-b70b-7ffd8ff9c04d\"><h2>Overview<\/h2>\n<p>After successfully aligning the rhodopsin sequences of the different species with the one from our newly discovered species in Part 3, we will construct a <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">phylogenetic tree <\/a>of the 21 rhodopsin proteins. A phylogenetic tree is a visual representation that illustrates the evolutionary relationships among different species. This is done by analysing variations in their genetic characteristics, such as differences in DNA and amino acid sequences.\u00a0<\/p>\n\n\n\n<p>To generate a phylogenetic tree based on our aligned input sequences, we can use the tool Simple Phylogeny.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-1eaf137f-ffdd-46e0-beee-42834893e5ab\"><h2>Your task<\/h2>\n<p><strong>Please follow the steps outlined below:<\/strong><\/p>\n\n\n\n<p><strong>1. <\/strong>Follow the instructions in the \u201cSimple Phylogeny\u201d tab.<\/p>\n\n\n\n<p><strong>2.<\/strong> Try to answer the questions in the \u201cQuestions\u201d tab.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-69241370-32fb-4b41-bb67-bfbd37b87933\"><h2>Simple Phylogeny<\/h2>\n<p><strong>1.<\/strong> Paste all the aligned amino acid sequences, including&nbsp; \u201cCLUSTAL O(1.2.4) multiple sequence alignment\u201d, into the input box (STEP 1) in the window below. (Alternatively, upload <a rel=\"noreferrer noopener\" href=\"https:\/\/drive.google.com\/file\/d\/1_QwQ9w6LzBDceP2LvVcHTS9yYrUIKfiP\/view?usp=sharing\" data-type=\"URL\" data-id=\"https:\/\/drive.google.com\/file\/d\/1_QwQ9w6LzBDceP2LvVcHTS9yYrUIKfiP\/view?usp=sharing\" target=\"_blank\">this FASTA file<\/a> containing the sequences from your computer.)<\/p>\n\n\n\n<p><strong>2.<\/strong> In STEP 2, keep the default settings.&nbsp;<\/p>\n\n\n\n<p><strong>3. <\/strong>Submit the aligned sequences for the phylogenetic tree generation.<\/p>\n\n\n\n<p><strong>4<\/strong>. Click on the \u201cPhylogenetic Tree\u201d tab. Results will be displayed as a \u201cCladogram\u201d as the default. Cladograms represent the branching patterns of species but do not indicate evolutionary time differences between groups. However, by selecting the branch length as &#8220;Real,&#8221; you can observe the time spans between branching points, which provides additional information in a &#8220;real&#8221; phylogenetic tree.<\/p>\n\n\n\n<p><strong>5. <\/strong>Analyse the phylogenetic tree structure and attempt to answer some of the task questions based on your observations.<\/p>\n\n\n\n<div class=\"vf-embed vf-embed--16x9 | vf-u-margin__bottom--400\"\n>\n<iframe src=\"https:\/\/www.ebi.ac.uk\/Tools\/phylogeny\/simple_phylogeny\/\" frameborder=\"0\" controls allowfullscreen><\/iframe><\/div>\n\n\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-00d9f095-46a3-40b6-84e5-e898498f61b3\"><h2>Questions<\/h2>\n<p><strong>1. <\/strong>Examine the &#8220;real&#8221; phylogenetic tree structure. Notice the two sequences that serve as an outgroup to all the others. Which species do these rhodopsin sequences belong to and what characteristics do you believe make them outliers?<br><strong>2. <\/strong>Observe the &#8220;cladogram&#8221; structure. The tree initially splits the sequences into three major groups. Does this split generally reflect the evolutionary relationships between the species? Are there any exceptions or inconsistencies?<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-5b32989c-1503-4b3e-90ed-b4adf182864e\"><h2>Activity navigation<\/h2>\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/\" target=\"_blank\" rel=\"noreferrer noopener\">Introductory page<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/embl.org\/ells\/teachingbase\/part-1-from-dna-to-protein-sequence\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 1: From DNA to protein sequence<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-2-protein-identity-and-function\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-2-protein-identity-and-function\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 2: Protein identity and function<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-3-multiple-sequence-alignment\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 3: Multiple sequence alignment&nbsp;<\/a><\/li>\n\n\n\n<li><a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-4-phylogenetic-analysis\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-4-phylogenetic-analysis\/\" target=\"_blank\"><strong>Part 4: Phylogenetic analysis&nbsp;<\/strong><\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-5-structural-analysis\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-5-structural-analysis\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 5: Structural analysis<\/a><\/li>\n<\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":36213,"parent":36087,"menu_order":4,"template":"","class_list":["post-36137","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/36137","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase"}],"about":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/types\/teachingbase"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/36087"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/36213"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=36137"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}