'Neighbor joining' presentation slideshows

Tree-building methods: Distance vs. Char

Tree-building methods: Distance vs. Char. Distance-based methods involve a distance metric, such as the number of amino acid changes between the sequences, or a distance score. Examples of distance-based algorithms are UPGMA and neighbor-joining.

1.49k views • 71 slides

Bioinformatics tools for phylogeny and visualization

Bioinformatics tools for phylogeny and visualization. Yanbin Yin Spring 2013. Homework assignment 5. Take the MAFFT alignment http :// cys.bios.niu.edu/yyin/teach/PBB/purdue.cellwall.list.lignin.fa.aln as input and use MEGA5 to build a phylogenetic tree

604 views • 58 slides

Phylogeny Tree Reconstruction

1. 4. 3. 5. 2. 5. 2. 3. 1. 4. Phylogeny Tree Reconstruction. Inferring Phylogenies. Trees can be inferred by several criteria: Morphology of the organisms Can lead to mistakes! Sequence comparison Example: Orc: A C A G T G A C G CCCC AAA C G T

557 views • 43 slides

Applied Bioinformatics

Applied Bioinformatics. Week 7 Jens Allmer. Practice I. Homework Feedback. Review Rough Writing Guidelines Word Template. Topic. Multiple Sequence Alignment Review Building an MSA Editing an MSA Dendrograms Phylogenetic Trees. Choosing Sequences. How many?

761 views • 42 slides

Phylogenetic trees

Phylogenetic trees. Phylogeny is the inference of evolutionary relationships. Traditionally, phylogeny relied on the comparison of morphological features between organisms. Today, molecular sequence data are mainly used for phylogenetic analyses. One tree of life A sketch Darwin made

1.41k views • 39 slides

Phylogenetic analysis

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CSCE555 Bioinformatics

CSCE555 Bioinformatics. Lecture 13 Phylogenetics II Meeting: MW 4:00PM-5:15PM SWGN2A21 Instructor: Dr. Jianjun Hu Course page: http://www.scigen.org/csce555. HAPPY CHINESE NEW YEAR. University of South Carolina Department of Computer Science and Engineering 2008 www.cse.sc.edu. Outline.

454 views • 36 slides

Phylogenetic Trees

Tutorial 6. Phylogenetic Trees. Tutorial 6. Phylogenetic Trees. Measuring distance Bottom-up algorithm (Neighbor Joining) Distance based algorithm Relative distance based. Measuring Distance.

448 views • 35 slides

Phylogenetic Trees

Tutorial 6. Phylogenetic Trees. Tutorial 6. Phylogenetic Trees. Measuring distance Bottom-up algorithm (Neighbor Joining) Distance based algorithm Relative distance based. Measuring Distance.

462 views • 33 slides

Gene expression and protein pathways

Gene expression and protein pathways. Joel S Bader CuraGen jsbader@curagen.com IPAM 2000 Nov 8. CuraGen Background. Product pipeline Therapeutic proteins Therapeutic antibodies Drug targets Technology High-throughput biology labs Bioinformatics/information-intensive. Outline.

423 views • 31 slides

Gene expression and protein pathways

Gene expression and protein pathways. Joel S Bader CuraGen jsbader@curagen.com IPAM 2000 Nov 8. CuraGen Background. Product pipeline Therapeutic proteins Therapeutic antibodies Drug targets Technology High-throughput biology labs Bioinformatics/information-intensive. Outline.

443 views • 31 slides

????: ???? ???? ???? ??????: ???? ????? Website: webcourse.cs.technion.ac.il/236503/

236503 ?????? ?????? ???? ??????? ?????? ??? ????????: ?????????? ?????? ??? ????? ?????? ???? 2013. ????: ???? ???? ???? ??????: ???? ????? Website: http://webcourse.cs.technion.ac.il/236503/. Evolution. Evolution of new organisms is driven by Diversity

436 views • 30 slides

Overview of Phylogeny

1. 4. 3. 5. 2. 5. 2. 3. 1. 4. Overview of Phylogeny. Edentata (anteaters, sloths, armadillos). New World monkeys. Old World monkeys. Lagomorpha (rabbits). humans, gorilla, chimpanzee, orangutan. Triconodonts. Rodentia (mice, rats, squirrels). gibbons. Multituberculata.

418 views • 28 slides

Phylogenetic Trees

Tutorial 5. Phylogenetic Trees. Agenda. How to construct a tree using Neighbor Joining algorithm Phylogeny.fr tool Cool story of the day: Horizontal gene transfer. Neighbor Joining Algorithm. Constructs an unrooted guide tree from a distance matrix

410 views • 26 slides

Phylogeny Tree Reconstruction

1. 4. 3. 5. 2. 5. 2. 3. 1. 4. Phylogeny Tree Reconstruction. Inferring Phylogenies. Trees can be inferred by several criteria: Morphology of the organisms Sequence comparison Example: Orc: A C A G T G A C G CCCC AAA C G T Elf: A C A G T G A C G C T A C AAA C G T

391 views • 25 slides

Phylogeny Tree Reconstruction

1. 4. 3. 5. 2. 5. 2. 3. 1. 4. Phylogeny Tree Reconstruction. Inferring Phylogenies. Trees can be inferred by several criteria: Morphology of the organisms Sequence comparison Example: Orc: A C A G T G A C G CCCC AAA C G T Elf: A C A G T G A C G C T A C AAA C G T

346 views • 25 slides

Wellcome Trust Workshop Working with Pathogen Genomes Module 6 Phylogeny

Wellcome Trust Workshop Working with Pathogen Genomes Module 6 Phylogeny. Phylogeny. Phylogeny refers to the ancestry of a biological lineage, but is also synonymous with phylogenetic tree Taxonomy began by grouping taxa together based on morphology at various structural levels

453 views • 24 slides

Distance-Based Approaches to Inferring Phylogenetic Trees

Distance-Based Approaches to Inferring Phylogenetic Trees. BMI/CS 576 www.biostat.wisc.edu/bmi576.html Colin Dewey cdewey@biostat.wisc.edu Fall 2010. Distance Based Approaches. given : an matrix where is the distance between taxa i and j

224 views • 21 slides

Testing Bacterial Proteins for Evidence of Horizontal Gene Transfer

Testing Bacterial Proteins for Evidence of Horizontal Gene Transfer. James Godde, John Iverson, Kabi Neupane, and Sara Penhale. Repetitive DNA. Found in abundance in Eukaryotes Only 1% of the human genome encodes protein, while more than half of the genome consists of repetitive DNA.

253 views • 14 slides

Gammaproteobacteria PmoA

A. C. B.

64 views • 5 slides