Phylogenetics

Phylogenetic inference is making a best estimate of the evolutionary history of a group of organisms based on the inheritance of ancestral characteristics. Until 50 years ago the study of evolution was carried out by studying differences in morphological characteristics between organisms, but now this science has become dominated (although not exclusively) by sequence data. Molecular phylogenetics converts the information in sequences into an evolutionary tree based on the similarities and/or differences between those sequences. Thus the more similar sequences are the closer they appear within a tree.

Phylogenetic trees obviously allow us to discover the evolutionary relationships among groups of organisms. However, trees are now recognized and are being used as a tool towards understanding biological processes. For example, conclusions may be drawn about the functions of a particular protein from its “relatedness” to other proteins of known function.

Services

Construction of Phylogenetic trees using:
- Distance
- Parsimony
- Maximum likelihood
- Quartets
- Bayesian methods

Sequence Assembly

Multiple sequence alignments
- Single Genes
- Concatenated Genes

Datasets Data Analysis and Interpretation
- Codon Usage
- Signs of Positive Selection

Topology Congruency Tests
- Partition Homogeneity
- Alternative Topology

Primer Design
- Including Degenerate Primers

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Introductory Phylogenetic Workshop

Hosted jointly by the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria and Inqaba Biotechnical Industries (Pty) Ltd.

The aim of this introductory workshop is to give a basic understanding of various phylogenetic techniques and to cover the steps required from checking a sequence to constructing a tree. It does not aim to cover absolutely everything there is “to know” or every piece of phylogenetic software ever written. The format is a mixture of presentations, exercises and discussions plus, tea, coffee and a light lunch.

Several topics will be covered and includes:

General principles
- Tree terminology
- Characters and character states
- Patterns in molecular datasets, including codon position/usage
- Heterogeneity, saturation etc.

Chromatograms and base calling

Consensus sequences

Data mining
- BLAST searches
- Sequence choice

Multiple sequence alignment:
- Comparison of different algorithms

Distance analysis
- Calculating a distance matrix
- Confidence in groupings, i.e. bootstrapping

Maximum Parsimony
- Synapomorphy, monophyly etc

Presentation of trees

For more information please follow this link

Bioinformatics

www.clcbio.com

CLC bio provides integrated bioinformatics solutions including sequence analysis software, high-performance computing, consulting, and education to pharmaceutical and biotechnology companies as well as hospitals and universities all over the world. We hereby facilitate research into genetically determined diseases, drug development, molecular diagnostics, agricultural research and more.

Products
Genomics Workbench
Main Workbench
DNA Workbench
RNA Workbench
Protein Workbench
Sequence Viewer

In-house Bioinformatics:

We have an in-house bioinformaticist Dr Hamilton Ganesan who is willing to assist with any of your bioinformatics needs, including project planning, implementation and high-throughput data analysis, high-performance bioinformatics laboratory set-ups etc For more details This e-mail address is being protected from spambots. You need JavaScript enabled to view it