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29 materials found

Keywords: Biomedical Literature  or Phylogenetics 


Discovering scientific evidence using Europe PMC SciLite annotation

For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find...

Keywords: Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer

Resource type: Life Sciences Literature Database

Discovering scientific evidence using Europe PMC SciLite annotation http://tess.elixir-uk.org/materials/discovering-scientific-evidence-using-europe-pmc-scilite-annotation For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find evidence in scientific literature. Who is this course for? This webinar is suitable for scientists, database curators or anyone who wishes to learn more about how to use annotations. Outcomes By the end of the webinar you will be able to: Explore Europe PubMed Central Use text mining for scientific literature searches Aravind Venkatesan Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer
Finding the data behind research publications with Europe PMC

This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis. Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints,...

Keywords: Biomedical Literature, Data links, databases, External links

Resource type: Life Sciences Literature Database

Finding the data behind research publications with Europe PMC http://tess.elixir-uk.org/materials/finding-the-data-behind-research-publications-with-europe-pmc This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis. Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more. Who is this course for? This webinar is aimed at scientists with an interest in learning more about the data-rich literature search tools provided by Europe PMC. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful. Michael Parkin Biomedical Literature, Data links, databases, External links
PGDH19 - Population Genetics Demographic History: model-based approaches (2019)

Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH19 - Population Genetics Demographic History: model-based approaches (2019) http://tess.elixir-uk.org/materials/pgdh19-population-genetics-demographic-history-model-based-approaches-2019 Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodriguez Vitor Sousa Armando Arredondo Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
PGDH18 - Population Genetics and Demographic History: model-based approaches (2018)

Training material for hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH18 - Population Genetics and Demographic History: model-based approaches (2018) http://tess.elixir-uk.org/materials/pgdh18-population-genetics-and-demographic-history-model-based-approaches-2018 Training material for hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodríguez Armando Arredondo Soto Vitor Sousa Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
Phylogenetics of animal viral pathogens

Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

Keywords: Animal pathogens, E learning, Phylogenetics

Resource type: e-learning

Phylogenetics of animal viral pathogens http://tess.elixir-uk.org/materials/phylogenetics-of-animal-viral-pathogens-428432a3-67ca-4284-8962-fefc2ade75db Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases. The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-Zone, Swiss-Prot Group at SIB Swiss Institute of Bioinformatics   Animal pathogens, E learning, Phylogenetics Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28
Navigating the data-rich literature: finding evidence in biomedical publications

In the age of data‐driven science, discovering all the data associated with a study can be tricky. In this webinar, we will demonstrate how to locate primary data in a publication, find facts and evidence to support your hypothesis, and scan a paper for important biological concepts using tools...

Keywords: Europe PMC, Biomedical Literature, Literature search

Resource type: Webinar

Navigating the data-rich literature: finding evidence in biomedical publications http://tess.elixir-uk.org/materials/navigating-the-data-rich-literature-finding-evidence-in-biomedical-publications In the age of data‐driven science, discovering all the data associated with a study can be tricky. In this webinar, we will demonstrate how to locate primary data in a publication, find facts and evidence to support your hypothesis, and scan a paper for important biological concepts using tools provided by Europe PMC. This webinar was recorded on 4th October 2017. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded here. This webinar is aimed at scientists with an interest in learning more about the literature search tools provided by Europe PMC. No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful. If you would like to learn more about Europe PMC have a look at our other webinar on Europe PMC: get the most from literature searches and our Europe PMC: Quick tour. See the EMBL-EBI training pages for a list of upcoming webinars. Europe PMC, Biomedical Literature, Literature search
Europe PMC: Services for academic authors

Researchers are often asked to maintain an up-to-date publication list, whether for job applications, tenure evaluations, or grant proposals. An easy way to do this is by using your ORCID iD and linking it to your published papers. An ORCID is a unique identifier - personalised number that is...

Keywords: Europe PMC, ORCID, Biomedical Literature

Resource type: Webinar

Europe PMC: Services for academic authors http://tess.elixir-uk.org/materials/europe-pmc-services-for-academic-authors Researchers are often asked to maintain an up-to-date publication list, whether for job applications, tenure evaluations, or grant proposals. An easy way to do this is by using your ORCID iD and linking it to your published papers. An ORCID is a unique identifier - personalised number that is assigned to you when you register. By using your ORCID in addition to your name you can make sure that you are easily distinguishable from other researchers with the same name, keep track of your work through name changes, and even pull together different kinds of achievements, like grant awards, training, etc. This video shows how you can register for an ORCID, add your publications in three easy steps to build your digital CV, and how to get a personal author profile page that showcases your publications and citations. This webinar was recorded on 7th of August 2017. It is best viewed in full-screen mode using Google Chrome. No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful. Europe PMC, ORCID, Biomedical Literature
Effective Literature Research with Europe PMC

Following the latest developments in your scientific field requires thorough and frequent literature research. In this webinar, we will show how to find and access relevant scientific literature using Europe PMC, an open biomedical literature database, part of PubMed Central International. We...

Keywords: Europe PMC, Biomedical Literature, Literature search

Resource type: Webinar

Effective Literature Research with Europe PMC http://tess.elixir-uk.org/materials/effective-literature-research-with-europe-pmc Following the latest developments in your scientific field requires thorough and frequent literature research. In this webinar, we will show how to find and access relevant scientific literature using Europe PMC, an open biomedical literature database, part of PubMed Central International. We will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries. This webinar was recorded on 30 May 2018. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded here. To learn more about searching grant information and on managing, exporting and saving searches you can watch our previous webinar Europe PMC: get the most from literature searches. You will find more information about Europe PMCs API service in our webinar Europe PMC, programmatically. You can also try our Europe PMC: Quick Tour. See the EMBL-EBI training pages for a list of upcoming webinars. This webinar is aimed at scientists who want to optimise their literature searches. No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful. Europe PMC, Biomedical Literature, Literature search Scientists who want to optimise their literature searches
Text mining: Key concepts and applications

EMBL-EBI presents this talk on an introduction to text mining and its applications in service provision. The 1st part of this talk focuses on what text mining is and some of the methods and available tools. The 2nd part looks at how to find articles on Europe PMC - a free literature resource for...

Keywords: Literature search, Text mining, Europe PMC, Biomedical Literature

Resource type: Webinar

Text mining: Key concepts and applications http://tess.elixir-uk.org/materials/text-mining-key-concepts-and-applications EMBL-EBI presents this talk on an introduction to text mining and its applications in service provision. The 1st part of this talk focuses on what text mining is and some of the methods and available tools. The 2nd part looks at how to find articles on Europe PMC - a free literature resource for biomedical and health researchers - and how to build your own text mining pipeline. The final part gives a nice case study showing how Europe PMC's pipeline was integrated into a new drug target validation platform called Open Targets (previously CTTV). Literature search, Text mining, Europe PMC, Biomedical Literature
Extracting research evidence from publications

Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature...

Keywords: Literature search, Biomedical Literature, Europe PMC, Text mining

Resource type: Webinar

Extracting research evidence from publications http://tess.elixir-uk.org/materials/extracting-research-evidence-from-publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation. Literature search, Biomedical Literature, Europe PMC, Text mining Wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically.
Europe PMC, programmatically

Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, books, patents, and clinical guidelines. More than 32 million abstracts (27 million from PubMed) and 4 million full-text articles can be freely accessed through Europe PMC in a single...

Keywords: Literature search, Programmatic Access, Europe PMC, REST API, Biomedical Literature

Resource type: Webinar

Europe PMC, programmatically http://tess.elixir-uk.org/materials/europe-pmc-programmatically Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, books, patents, and clinical guidelines. More than 32 million abstracts (27 million from PubMed) and 4 million full-text articles can be freely accessed through Europe PMC in a single search. The mission of Europe PMC is to build open access, full-text scientific literature resources and deliver world-class literature services. This webinar will introduce the Europe PMC Articles RESTful API and show you how to access publications and related information, such as citations, data links, or text-mined terms, programmatically. Francesco Talo Yogmatee Rochun Literature search, Programmatic Access, Europe PMC, REST API, Biomedical Literature
Introducing Bivi.co

Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations

Resource type: Video

Introducing Bivi.co http://tess.elixir-uk.org/materials/introducing-bivi-co Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting. Created at: 1st BiVi Annual Meeting. Prof. Jessie Kennedy Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations 2016-12-08
Jalview

Dr James Proctor of the University of Dundee discusses the Jalview tool in the Vis Tools & Bio Challenges session of the 1st BiVi Annual Meeting Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Molecular, Phylogenetics

Resource type: Poster, Video

Jalview http://tess.elixir-uk.org/materials/jalview Dr James Proctor of the University of Dundee discusses the Jalview tool in the Vis Tools & Bio Challenges session of the 1st BiVi Annual Meeting Created at: 1st BiVi Annual Meeting. Dr. Jim Procter Jalview Coordinator Phylogenetics Genome, Molecular, Phylogenetics 2016-12-08
BiVi Genomes theme

Prof David Burt introduces the Genomes theme in bio-visualisation. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Video

BiVi Genomes theme http://tess.elixir-uk.org/materials/bivi-genomes-theme Prof David Burt introduces the Genomes theme in bio-visualisation. Created at: 1st BiVi Annual Meeting. Prof. David Willaim Burt PhD BSc FSB Phylogenetics Genome, Phylogenetics 2016-12-08
Metagenomics

Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but more effort into...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics, Populations

Resource type: Video

Metagenomics http://tess.elixir-uk.org/materials/metagenomics-6625dde2-a7da-4cc2-a51d-14c1c31b51b2 Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but more effort into analysis and visualisation solutions are required at the microbial community and ecosystem level.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Phylogenetics Genome, Phylogenetics, Populations 2017-01-31
Geographic & Evolutionary Visualization

Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013.

Scientific topics: Phylogenetics

Keywords: Phylogenetics, Populations

Resource type: Video

Geographic & Evolutionary Visualization http://tess.elixir-uk.org/materials/geographic-amp-evolutionary-visualization Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Phylogenetics Phylogenetics, Populations 2017-01-31
BBSRC: Data and Data Visualisation

Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation

Resource type: Video

BBSRC: Data and Data Visualisation http://tess.elixir-uk.org/materials/bbsrc-data-and-data-visualisation Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Michael Ball Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation 2017-02-01
BiVi theme: Phylogenetics

Prof Rod Page discusses bio-visualisation and the Phylogenetics theme at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Phylogenetics

Resource type: Video

BiVi theme: Phylogenetics http://tess.elixir-uk.org/materials/bivi-theme-phylogenetics Prof Rod Page discusses bio-visualisation and the Phylogenetics theme at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Prof. Rod Page Phylogenetics Phylogenetics 2017-02-02
Aequatus-vis

Anil Thanki describes the Aequatus-vis JavaScript plugin to visualise homologous genes through alignment and phylogeny information at 2nd BiVi in 2015. aequatus-vis preserves teh interactive functionality of Aequatus, an open-source web based tool to visualise homologous genes with phylogenetic...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

Aequatus-vis http://tess.elixir-uk.org/materials/aequatus-vis Anil Thanki describes the Aequatus-vis JavaScript plugin to visualise homologous genes through alignment and phylogeny information at 2nd BiVi in 2015. aequatus-vis preserves teh interactive functionality of Aequatus, an open-source web based tool to visualise homologous genes with phylogenetic tree . Created at: 2nd BiVi Annual Meeting. Anil S. Thanki Phylogenetics Genome, Phylogenetics 2017-02-03
Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles

Roland Schwarz's keynote about the joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles http://tess.elixir-uk.org/materials/joint-visualisation-and-analysis-of-large-sequence-data-with-alvis-and-sequence-bundles Roland Schwarz's keynote about the joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Dr. Roland Schwarz Phylogenetics Genome, Phylogenetics 2017-02-03
BioJS

Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics

Resource type: Video

BioJS http://tess.elixir-uk.org/materials/biojs-6f4125d4-aca1-407d-b0c7-02345f3b3900 Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014. Created at: 1st BiVi Annual Meeting. Dr. Manuel Corpas Phylogenetics Pathway or network Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics 2016-12-08
Art and Science: A partnership catalyzing discovery in biomedicine

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation

Resource type: Video

Art and Science: A partnership catalyzing discovery in biomedicine http://tess.elixir-uk.org/materials/art-and-science-a-partnership-catalyzing-discovery-in-biomedicine A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. Bang will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.Bang Wong is the creative director of the Broad Institute of MIT & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science. Created at: 3rd BiVi Annual Meeting (2017). Bang Wong Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation 2017-05-12
ViCTree-Virus Taxonomy Classification Framework

Poster presentation at 3rd BiVi in April 2017. Created at: 3rd BiVi Annual Meeting (2017).

Scientific topics: Phylogenetics

Keywords: Phylogenetics

Resource type: Poster

ViCTree-Virus Taxonomy Classification Framework http://tess.elixir-uk.org/materials/victree-virus-taxonomy-classification-framework Poster presentation at 3rd BiVi in April 2017. Created at: 3rd BiVi Annual Meeting (2017). Ms. Sejal Modha Phylogenetics Phylogenetics 2017-05-30
Phylogenetics & Phylogeography (Advanced Analytical Methods)

Phylogenetics and Phylogeography(Advanced Analytical Methods) Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015.

Keywords: Phylogenetics, Roslin Institute

Phylogenetics & Phylogeography (Advanced Analytical Methods) http://tess.elixir-uk.org/materials/phylogenetics-phylogeography-advanced-analytical-methods Phylogenetics and Phylogeography(Advanced Analytical Methods) Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015. Phylogenetics, Roslin Institute
Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)

Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015.

Keywords: Phylogenetics, Phylogeography, Roslin Institute

Phylogenetics & Phylogeography Practical (Advanced Analytical Methods) http://tess.elixir-uk.org/materials/phylogenetics-phylogeography-practical-advanced-analytical-methods Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015. Phylogenetics, Phylogeography, Roslin Institute
UPGMA Worked Example

A walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calculated. A small CGI...

Keywords: Molecular phylogeny, Phylogenetics, Upgma

UPGMA Worked Example http://tess.elixir-uk.org/materials/upgma-worked-example A walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calculated. A small CGI site for generating a UPGMA tree from a distance matrix can be found here. The source data for this worked example is a subset of Cytochrome C distances from Table 3 of one of the seminal phylogenetic papers: Fitch WM & Margoliash E (1967). Construction of phylogenetic trees. Science 155:279-84. PowerPoint timings are set up to be consistent with autolooping the presentation. Molecular phylogeny, Phylogenetics, Upgma Beginners 2014-08-04 2017-10-09
Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies http://tess.elixir-uk.org/materials/introduction-to-multiple-sequence-alignments-msas-and-phylogenies Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood. Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment Bench biologists Post-Doctoral Fellows Postgraduate students principle investigators 2013-12-19 2017-10-09
Summarising sets of phylogenies

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

Keywords: Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics

Summarising sets of phylogenies http://tess.elixir-uk.org/materials/summarising-sets-of-phylogenies A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes examples of applications of these tools, along with introducing ideas of tree topology and some terminology associated with it. Designed for remote training. Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics Bench biologists 2013-10-23 2017-10-09
Interpreting Phylogenies

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...

Keywords: Molecular evolution, Phylogenetics

Interpreting Phylogenies http://tess.elixir-uk.org/materials/interpreting-phylogenies Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic trees. Includes exercises on visulaising and manipulating trees using Dendroscope and NJplot to reinforce some of these ideas, while also providing a very basic overview of steps involved in a generic phylogenetic analysis. Molecular evolution, Phylogenetics experimeintal biologist researchers field biologist researchers 2013-09-13 2017-10-09