{"showCoverPage":true,"bookCover":{"coverDescription":"

<\/p>\n\n

PHYLOGENETIC ANALYSIS<\/strong><\/p>\n\n

<\/p>\n\n

By<\/p>\n\n

S.NARMATHA<\/strong><\/p>\n\n

Assistant Professor<\/p>\n\n

Department of Plant Biology and Plant Biotechnology (SS)<\/p>\n\n

Ethiraj College for Women<\/p>\n\n

Chennai-600008<\/p>\n\n

Tamil Nadu<\/p>\n\n

India<\/p>\n","coverMedium":{"library":"H5P.Image 1.1","metadata":{"contentType":"Image","license":"CC BY","title":"Bioinformatics","authors":[{"name":"EMBL-EBI\u2019s resources and databases","role":"Author"}],"source":"https:\/\/www.oercommons.org\/courses\/a-journey-through-bioinformatics-explore-resources-from-embl-ebi\/view","licenseVersion":"4.0"},"params":{"contentName":"Image","decorative":false,"alt":"BIOINFORMATICS","file":{"path":"images\/image-Bgg4JpjT.png","mime":"image\/png","width":1536,"height":776}},"subContentId":"d0e26f85-51d4-4f1c-bd6d-8143a28b49bd"}},"chapters":[{"params":{"content":[{"content":{"library":"H5P.CoursePresentation 1.24","params":{"presentation":{"slides":[{"elements":[{"x":16.738144835191765,"y":33.4766317134807,"width":72.12964097537066,"height":35.77618342192659,"action":{"library":"H5P.AdvancedText 1.1","params":{"text":"

<\/h2>\n\n
BIOINFORMATICS<\/strong><\/span><\/span><\/h2>\n"},"metadata":{"contentType":"Text","license":"U","title":"Untitled Text"},"subContentId":"c1e370a9-055b-4ced-80ca-94ba7da2ceb0"},"alwaysDisplayComments":false,"backgroundOpacity":0,"displayAsButton":false,"buttonSize":"big","goToSlideType":"specified","invisible":false,"solution":""}],"slideBackgroundSelector":{}},{"elements":[{"x":3.2240748114319246,"y":12.737595969824635,"width":94.9320251781251,"height":86.30039709455436,"action":{"library":"H5P.AdvancedText 1.1","params":{"text":"
INTRODUCTION<\/strong><\/span><\/span><\/h3>\n\n
\n\t
\n\t
Bioinformatics \u2013 Information technology applied to the management & analysis of biological data<\/span> <\/strong><\/p>\n\t<\/li>\n\t
\n\t
Large amount of sequence data related to various living organisms \u2013 collected & stored in databases.<\/span><\/strong><\/p>\n\t<\/li>\n\t
\n\t
It is not very convenient to compare the sequences of several hundred nucleotides & aminoacids by hand.<\/span><\/strong><\/p>\n\t<\/li>\n\t
\n\t
Several computational techniques were developed.<\/span><\/strong><\/p>\n\t<\/li>\n\t
\n\t
Data can be faster than they can be analyzed & utilized.<\/span><\/strong><\/p>\n\t<\/li>\n\t
\n\t
Need for professionals \u2013 software<\/span><\/strong><\/p>\n\t<\/li>\n<\/ul>\n"},"subContentId":"d4166e9f-cebf-4cbb-aca5-9483426d54c1","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"}},"alwaysDisplayComments":false,"backgroundOpacity":0,"displayAsButton":false,"buttonSize":"big","goToSlideType":"specified","invisible":false,"solution":""}],"slideBackgroundSelector":{}},{"elements":[{"x":3.2916392363396967,"y":16.255563466596442,"width":95.4575378538512,"height":78.02670463966292,"action":{"library":"H5P.AdvancedText 1.1","params":{"text":"
What is Bioinformatics <\/span><\/span><\/h3>\n\n
\n\t
Bioinformatics is the science of storing, retrieving and analysing large amounts of biological information. <\/strong><\/span><\/li>\n\t
It is a highly interdisciplinary field involving many different types of specialists, including biologists, molecular life scientists, computer scientists and mathematicians.<\/strong><\/span><\/li>\n<\/ul>\n"},"metadata":{"contentType":"Text","license":"U","title":"Untitled Text"},"subContentId":"7fcb6990-7689-4645-a915-dac2f59d2d31"},"alwaysDisplayComments":false,"backgroundOpacity":0,"displayAsButton":false,"buttonSize":"big","goToSlideType":"specified","invisible":false,"solution":""}],"slideBackgroundSelector":{}},{"elements":[{"x":4.674807260256604,"y":12.737595969824635,"width":95.32601680580301,"height":83.30196700325764,"action":{"library":"H5P.AdvancedText 1.1","params":{"text":"
<\/p>\n\n
Bioinformatics in life science<\/span><\/span><\/h2>\n\n
\n\t
\n\t
Genome sequencing is the major break - Genome of several organisms, including human are sequenced, mapped & stored in database.<\/span><\/p>\n\t<\/li>\n\t
\n\t
Genome databases provide \u2013 advance in medical biotechnology, Genetics, Evolutionary studies etc.<\/span><\/p>\n\t<\/li>\n\t
\n\t
Diseases related, mutation gene diversity in ecosystem<\/span><\/p>\n\t<\/li>\n\t
\n\t
Sequence, folding patterns, secondary structure, domain & 3D<\/span><\/p>\n\t<\/li>\n\t
\n\t
Metabolic pathway of a cell, Nanotechnology<\/span><\/p>\n\t<\/li>\n<\/ul>\n"},"subContentId":"6ea33b16-8425-40b2-8ebf-bece563e898a","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"}},"alwaysDisplayComments":false,"backgroundOpacity":0,"displayAsButton":false,"buttonSize":"big","goToSlideType":"specified","invisible":false,"solution":""}],"slideBackgroundSelector":{}},{"elements":[{"x":3.2240748114319246,"y":12.737595969824635,"width":93.4801467168169,"height":72.77020421550738,"action":{"library":"H5P.AdvancedText 1.1","params":{"text":"
BIOINFORMATICS<\/span><\/span><\/strong><\/h2>\n\n
\n\t
\n\t
It is the application of IT \u2013 management & analysis of biological data<\/strong><\/span><\/p>\n\t<\/li>\n\t
\n\t
The term Bioinformatics was coined by Pauline Hogeweg \u2013 1978.<\/strong><\/span><\/p>\n\t<\/li>\n\t
\n\t
Several interpretations for bioinformatics.<\/strong><\/span><\/p>\n\t<\/li>\n\t
\n\t
Science of informatics is concerned with representation, organization, manipulation, distribution, maintenance & use of information particularly in digital form<\/strong><\/span><\/p>\n\t<\/li>\n\t
\n\t
Discipline of quantitative analysis of information relating to biological macromolecules with the aid of computers.<\/strong><\/span><\/p>\n\t<\/li>\n<\/ul>\n"},"subContentId":"730afe62-d5ff-4bdf-8037-0f808a3d4b84","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"}},"alwaysDisplayComments":false,"backgroundOpacity":0,"displayAsButton":false,"buttonSize":"big","goToSlideType":"specified","invisible":false,"solution":""}],"slideBackgroundSelector":{}},{"elements":[{"x":3.2188858470417636,"y":13.692915667561484,"width":96.46099595546994,"height":78.84380841381902,"action":{"library":"H5P.AdvancedText 1.1","params":{"text":"
Steps in Bioinformatics<\/span><\/span><\/h2>\n\n
1. Development of new algorithms & statistics to access relationship of large data<\/strong><\/span><\/p>\n\n
<\/p>\n\n
2. Analysis & interpretation of data nucleotide protein sequence<\/span><\/strong><\/p>\n\n
<\/p>\n\n
3. Development & implementation of tools<\/span><\/strong><\/p>\n\n
<\/p>\n"},"subContentId":"3bfd1d4f-7f56-48ed-9083-9ca0788ccfb8","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"}},"alwaysDisplayComments":false,"backgroundOpacity":0,"displayAsButton":false,"buttonSize":"big","goToSlideType":"specified","invisible":false,"solution":""}],"slideBackgroundSelector":{}},{"elements":[{"x":6.609353363435446,"y":15.603555063035179,"width":83.0673728902215,"height":79.16224831306464,"action":{"library":"H5P.AdvancedText 1.1","params":{"text":"
<\/p>\n\n
<\/p>\n\n
Importance of Bioinformatics<\/span><\/span><\/h2>\n\n
\n\t
\n\t
Gained through human genome project.<\/span><\/p>\n\t<\/li>\n\t
\n\t
Storing, searching & distribution of biological data.<\/span><\/p>\n\t<\/li>\n\t
\n\t
Molecular structure, function & evolution.<\/span><\/p>\n\t<\/li>\n\t
\n\t
Drug designing, protein engineering, phylogenetic analyzing<\/span><\/p>\n\t<\/li>\n<\/ul>\n"},"subContentId":"fd231ece-0349-4cad-ba4d-e726b9dcebcc","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"}},"alwaysDisplayComments":false,"backgroundOpacity":0,"displayAsButton":false,"buttonSize":"big","goToSlideType":"specified","invisible":false,"solution":""}],"slideBackgroundSelector":{}}],"keywordListEnabled":true,"globalBackgroundSelector":{"imageGlobalBackground":{"path":"images\/image-82f7iX3O.png","mime":"image\/png","copyright":{"license":"U"},"width":1698,"height":820}},"keywordListAlwaysShow":false,"keywordListAutoHide":false,"keywordListOpacity":90},"override":{"activeSurface":false,"hideSummarySlide":false,"summarySlideSolutionButton":true,"summarySlideRetryButton":true,"enablePrintButton":false,"social":{"showFacebookShare":false,"facebookShare":{"url":"@currentpageurl","quote":"I scored @score out of @maxScore on a task at @currentpageurl."},"showTwitterShare":false,"twitterShare":{"statement":"I scored @score out of @maxScore on a task at @currentpageurl.","url":"@currentpageurl","hashtags":"h5p, course"},"showGoogleShare":false,"googleShareUrl":"@currentpageurl"}},"l10n":{"slide":"Slide","score":"Score","yourScore":"Your Score","maxScore":"Max Score","total":"Total","totalScore":"Total Score","showSolutions":"Show solutions","retry":"Retry","exportAnswers":"Export text","hideKeywords":"Hide sidebar navigation menu","showKeywords":"Show sidebar navigation menu","fullscreen":"Fullscreen","exitFullscreen":"Exit fullscreen","prevSlide":"Previous slide","nextSlide":"Next slide","currentSlide":"Current slide","lastSlide":"Last slide","solutionModeTitle":"Exit solution mode","solutionModeText":"Solution Mode","summaryMultipleTaskText":"Multiple tasks","scoreMessage":"You achieved:","shareFacebook":"Share on Facebook","shareTwitter":"Share on Twitter","shareGoogle":"Share on Google+","summary":"Summary","solutionsButtonTitle":"Show comments","printTitle":"Print","printIngress":"How would you like to print this presentation?","printAllSlides":"Print all slides","printCurrentSlide":"Print current slide","noTitle":"No title","accessibilitySlideNavigationExplanation":"Use left and right arrow to change slide in that direction whenever canvas is selected.","accessibilityCanvasLabel":"Presentation canvas. Use left and right arrow to move between slides.","containsNotCompleted":"@slideName contains not completed interaction","containsCompleted":"@slideName contains completed interaction","slideCount":"Slide @index of @total","containsOnlyCorrect":"@slideName only has correct answers","containsIncorrectAnswers":"@slideName has incorrect answers","shareResult":"Share Result","accessibilityTotalScore":"You got @score of @maxScore points in total","accessibilityEnteredFullscreen":"Entered fullscreen","accessibilityExitedFullscreen":"Exited fullscreen","confirmDialogHeader":"Submit your answers","confirmDialogText":"This will submit your results, do you want to continue?","confirmDialogConfirmText":"Submit and see results"}},"metadata":{"defaultLanguage":"en","license":"CC BY","title":"What is Bioinformatics","authors":[{"name":"S.NARMATHA","role":"Author"}],"contentType":"Course Presentation","licenseVersion":"4.0","source":"https:\/\/www.oercommons.org\/search?f.search=bioinformatics"},"subContentId":"9d88ee75-73b1-419a-b74d-13ca85f9703a"},"useSeparator":"auto"},{"content":{"params":{"media":{"disableImageZooming":false},"answers":[{"correct":false,"tipsAndFeedback":{"tip":"","chosenFeedback":"","notChosenFeedback":""},"text":"
J D Watson<\/div>\n"},{"correct":false,"tipsAndFeedback":{"tip":"","chosenFeedback":"","notChosenFeedback":""},"text":"
Margaret Dayhoff<\/div>\n"},{"correct":true,"tipsAndFeedback":{"tip":"","chosenFeedback":"","notChosenFeedback":""},"text":"
Pauline Hogeweg<\/div>\n"},{"correct":false,"tipsAndFeedback":{"tip":"","chosenFeedback":"","notChosenFeedback":""},"text":"
Frederic Sanger<\/div>\n"}],"overallFeedback":[{"from":0,"to":100}],"behaviour":{"enableRetry":true,"enableSolutionsButton":true,"enableCheckButton":true,"type":"single","singlePoint":false,"randomAnswers":true,"showSolutionsRequiresInput":true,"confirmCheckDialog":false,"confirmRetryDialog":false,"autoCheck":false,"passPercentage":60,"showScorePoints":true},"UI":{"checkAnswerButton":"Check","submitAnswerButton":"Submit","showSolutionButton":"Show solution","tryAgainButton":"Retry","tipsLabel":"Show tip","scoreBarLabel":"You got :num out of :total points","tipAvailable":"Tip available","feedbackAvailable":"Feedback available","readFeedback":"Read feedback","wrongAnswer":"Wrong answer","correctAnswer":"Correct answer","shouldCheck":"Should have been checked","shouldNotCheck":"Should not have been checked","noInput":"Please answer before viewing the solution","a11yCheck":"Check the answers. The responses will be marked as correct, incorrect, or unanswered.","a11yShowSolution":"Show the solution. The task will be marked with its correct solution.","a11yRetry":"Retry the task. Reset all responses and start the task over again."},"confirmCheck":{"header":"Finish ?","body":"Are you sure you wish to finish ?","cancelLabel":"Cancel","confirmLabel":"Finish"},"confirmRetry":{"header":"Retry ?","body":"Are you sure you wish to retry ?","cancelLabel":"Cancel","confirmLabel":"Confirm"},"question":"
1. The term bioinformatics was coined by<\/p>\n"},"library":"H5P.MultiChoice 1.16","metadata":{"contentType":"Multiple Choice","license":"CC BY","title":"BIOINFORMATICS","authors":[{"name":"S.NARMATHA","role":"Author"}],"licenseVersion":"4.0"},"subContentId":"da4faf11-70cc-445e-9c2a-331df1ad5543"},"useSeparator":"auto"}]},"library":"H5P.Column 1.15","subContentId":"10e179d0-d331-4f92-9d58-f372610d536f","metadata":{"contentType":"Column","license":"CC BY","title":"INTRODUCTION","authors":[{"name":"Firstname Surname","role":"Author"},{"name":"Narmatha","role":"Author"}],"licenseVersion":"4.0","source":"https:\/\/www.oercommons.org\/courses\/bioinformatics-for-the-terrified-an-introduction-to-the-science-of-bioinformatics\/view"}},{"params":{"content":[{"content":{"params":{"text":"
What is phylogenetics?<\/span><\/span><\/strong><\/h2>\n\n
Phylogenetics is the study of evolutionary relationships among biological entities \u2013 often species, individuals or genes (which may be referred to as taxa). <\/p>\n\n
Typically phylogeneticists study one of the following types of question:<\/strong><\/p>\n\n
\n\t
What are the evolutionary relationships or histories among my species\/individuals\/genes of interest?<\/li>\n\t
How do sequences evolve?<\/li>\n\t
Can I better describe processes of sequence evolution with a mathematical model<\/li>\n<\/ul>\n\n
Phylogenetic analysis helps to understand<\/strong><\/p>\n\n
\n\t
Similarity among species or individuals<\/li>\n\t
Dissimilarity between species<\/li>\n\t
Evolutionary distance between the species<\/li>\n\t
Possible ancestor of a group<\/li>\n<\/ul>\n\n
<\/p>\n"},"library":"H5P.AdvancedText 1.1","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"},"subContentId":"30690f9c-d159-4303-949e-a5eec1dcaab9"},"useSeparator":"auto"},{"content":{"params":{"linkWidget":{"protocol":"http:\/\/","url":"www.jse.ac.cn\/EN\/10.3724\/SP.J.1002.2008.08060"},"title":"Phylogenetic analysis"},"library":"H5P.Link 1.3","metadata":{"contentType":"Link","license":"U"},"subContentId":"3bd2b2ce-7710-46e2-8905-175926fa8cbc"},"useSeparator":"auto"}]},"library":"H5P.Column 1.15","subContentId":"b732c41f-df2a-4d0a-b5af-fcc1615e21e4","metadata":{"contentType":"Column","license":"CC BY","title":"PHYLOGENETIC","authors":[{"name":"S.NARMATHA","role":"Author"}],"licenseVersion":"4.0","source":"https:\/\/www.oercommons.org\/courses\/bioinformatics-for-the-terrified-an-introduction-to-the-science-of-bioinformatics\/view"}},{"params":{"content":[{"content":{"params":{"text":"
Phylogenetic tree<\/strong><\/span><\/h2>\n\n
\n\t
Tree like graph that shows ancestral relationship among various species originated from a common ancestor is called phylogenetic tree or evolutionary tree<\/strong><\/span><\/li>\n\t
It is a two dimensional graph <\/strong><\/span><\/li>\n\t
Phylogenetic tree is built from morphological data (fruit shape, flower colour) or molecular data (DNA , RNA, Protein sequence)<\/strong><\/span><\/li>\n<\/ul>\n\n
Structure of typical Phylogenetic tree <\/strong><\/span><\/span><\/h3>\n\n
\n\t
Root<\/strong><\/span><\/li>\n\t
Node <\/strong><\/span><\/li>\n\t
Branches<\/strong><\/span><\/li>\n\t
Taxa<\/span><\/li>\n<\/ul>\n\n
Types of phylogenetic tree <\/strong><\/span><\/span><\/p>\n\n
\n\t
Phenogram<\/strong><\/span><\/li>\n\t
Cladogram<\/strong><\/span><\/li>\n<\/ul>\n\n
PHYLOGENETIC TREE<\/strong><\/span><\/h2>\n\n
<\/p>\n"},"library":"H5P.AdvancedText 1.1","metadata":{"contentType":"Text","license":"CC BY","title":"PHYLOGENETIC TREE","authors":[{"name":"S.NARMATHA","role":"Author"}],"licenseVersion":"4.0"},"subContentId":"fff65dee-3ec9-4876-b921-546eba794dc3"},"useSeparator":"auto"},{"content":{"params":{"contentName":"Image","alt":"Phylogenetic tree","file":{"path":"images\/file-622a2dfbd1d5e.png","mime":"image\/png","copyright":{"license":"U"},"width":1024,"height":851}},"library":"H5P.Image 1.1","metadata":{"contentType":"Image","license":"CC BY-NC-SA","title":"Phylogenetic tree","authors":[{"name":"Firstname Surname","role":"Author"},{"name":"Sudaralingam, Kumaresan","role":"Author"}],"licenseVersion":"3.0","source":"https:\/\/bio.libretexts.org\/Bookshelves\/Microbiology\/Book%3A_Microbiology_(Bruslind)\/16%3A_Taxonomy_and_Evolution"},"subContentId":"1ba024d2-ed9b-466c-851f-984abcff19c2"},"useSeparator":"auto"}]},"library":"H5P.Column 1.15","subContentId":"78ee3216-afbf-49b2-9e17-c9ac5d4e5176","metadata":{"contentType":"Column","license":"CC BY","title":"Phylogenetic tree","authors":[{"name":"S.NARMATHA","role":"Author"}],"source":"https:\/\/www.oercommons.org\/courses\/phylogenetics-an-introduction\/view","licenseVersion":"4.0"}},{"params":{"content":[{"content":{"params":{"text":"
1.Phenogram<\/strong><\/span><\/span><\/p>\n\n
Click on the + button <\/span><\/strong><\/p>\n"},"library":"H5P.AdvancedText 1.1","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"},"subContentId":"7b375804-0eb7-4da6-928b-5827e851b27c"},"useSeparator":"auto"},{"content":{"params":{"iconType":"icon","icon":"plus","color":"#ee1649","hotspotNumberLabel":"Hotspot #num","closeButtonLabel":"Close","hotspots":[{"position":{"x":52.800000000000004,"y":40.88184545460011},"alwaysFullscreen":false,"content":[{"params":{"text":"
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2.Cladogram <\/strong><\/span><\/span><\/p>\n\n
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Cladogram branches are radiating outward from the central point<\/strong><\/h3>\n"},"library":"H5P.Text 1.1","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"},"subContentId":"3bd86ba2-649b-4c6d-81f0-7f28d149f5e0"}]}],"hotspotNumberLabel":"Hotspot #num","closeButtonLabel":"Close","image":{"path":"images\/image-Ldrus3rf.png","mime":"image\/png","copyright":{"license":"CC BY-SA","version":"4.0","source":"https:\/\/www.oercommons.org\/courses\/phylogenetics-an-introduction\/view"},"width":287,"height":200,"originalImage":{"path":"images\/image-M4RSlLHR.png","mime":"image\/png","height":469,"width":383}}},"library":"H5P.ImageHotspots 1.10","metadata":{"contentType":"Image Hotspots","license":"U","title":"CLADOGRAM"},"subContentId":"c37ecf13-2756-44cb-8d0c-0bb02d3ab4da"},"useSeparator":"auto"}]},"library":"H5P.Column 1.15","subContentId":"a40204f3-e9c0-46c6-ba8e-dd4b01c62383","metadata":{"contentType":"Column","license":"CC BY","title":"Phenogram and cladogram","authors":[{"name":"Firstname Surname","role":"Author"},{"name":"S.NARMATHA","role":"Author"}],"licenseVersion":"4.0","source":"https:\/\/www.oercommons.org\/courses\/phylogenetics-an-introduction\/view"}},{"params":{"content":[{"content":{"params":{"taskDescription":"
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Taxa<\/p>\n"},"subContentId":"ebb9c4a9-3f1a-4452-84ac-04bcc5fad533","metadata":{"contentType":"Text","license":"U","title":"Untitled Text"}},"backgroundOpacity":100,"multiple":false}],"dropZones":[{"x":21.786756073058257,"y":83.00017983372297,"width":6.272478399122996,"height":2.499349639394605,"correctElements":["0"],"showLabel":false,"backgroundOpacity":100,"tipsAndFeedback":{"tip":""},"single":true,"autoAlign":true,"label":"
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Phylogeny Programs<\/strong><\/span><\/span><\/h2>\n\n
\n\t
PHYLIP<\/a><\/li>\n\t
PAUP<\/a><\/li>\n\t
MEGA<\/a><\/li>\n\t
Phylo_win<\/a><\/li>\n\t
ARB<\/a><\/li>\n\t
DAMBE<\/a><\/li>\n\t
PAL<\/a><\/li>\n\t
Bionumerics<\/a><\/li>\n\t
Mesquite<\/a><\/li>\n\t
PaupUp<\/a><\/li>\n\t
BIRCH<\/a><\/li>\n\t
Bosque<\/a><\/li>\n\t
EMBOSS<\/a><\/li>\n\t
phangorn<\/a><\/li>\n\t
Bio++<\/a><\/li>\n\t
ETE<\/a><\/li>\n\t
DendroPy<\/a><\/li>\n\t
SeaView<\/a><\/li>\n\t
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