Register training material
25 materials found

Keywords: Phylogenetics 


WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset

This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021.

Hybridisation plays an important role in evolution, leading to the exchange of genes...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.

Multi-gene datasets used in phylogenetic...

Keywords: Phylogenetics, Bioinformatics, Phylogeny, Genomics, Target capture sequencing

PGDH19 - Population Genetics Demographic History: model-based approaches (2019)

Genetic and genomic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the...

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH18 - Population Genetics and Demographic History: model-based approaches (2018)

Genetic and genomic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the...

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

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

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: Pathway or network, Phylogenetics

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

Resource type: Video

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

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

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

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

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: Pathway or network, Phylogenetics

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

Resource type: Video

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

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

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

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: Pathway or network, Phylogenetics

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

Resource type: Video

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: Pathway or network, Phylogenetics

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

Resource type: Video

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

A Simple Phylogenetic Tree Construction (part 2)

Understand the method used in identifying an unknown sequence.
Understand the limitations of this method
Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot)

Keywords: Phylogenetics

A Simple Phylogenetic Tree Construction (part 1)

Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree.
Get to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win).

Keywords: Phylogenetics

Phylogenetics & Phylogeography (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography (lecture-part 1)

  2. Phylogenetics & Phylogeography (lecture-part 2)

  3. Phylogenetics & Phylogeography (lecture-part 3)

  4. Phylogenetics & Phylogeography (lecture-part 4)

  5. Phylogenetics & Phylogeography (lecture-part 5)

6....

Keywords: Phylogenetics, Roslin Institute

Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography Practical - Overview

  2. Phylogenetics & Phylogeography Practical 1

  3. Phylogenetics & Phylogeography Practical 2 - Part 1

  4. Phylogenetics & Phylogeography Practical 2 - Part 2

  5. Phylogenetics & Phylogeography Practical 3

6....

Keywords: 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

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

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

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