Action for Building Capacity (ABC) Fogarty Workshops:
Introduction to HIV Sequencing and Phylogenetic Analysis.
9 to 13 of February 2004, Durban, South Africa.

Workshop Material for the HIV Subtyping and Recombination Analysis Lecture
Back to the workshop home page

Reference Sequence:

Sequences for subtyping lecture: seq1.fasta , seq2.fasta, seq3.fasta
Sequences for recombination lecture: rec1.fasta, rec2.fasta, rec3.fasta       

  
Reference Dataset for Phylogenetic Analysis:

28 sequences (Subtype A - K, and outgroup O)
 
Basic Analysis for a new DNA sequence

Contamination: (more than 98 % similarity suggest recombinatipn)
Genomic Region Identification:

HIV Subtyping Analysis:
Recombination:
Links for the Programs used in the Workshop:

  • PAUP*  - Phylogenetics software.
  • ClustalX - alignment software.
  • GeneDoc - Sequence Visualization software.
  • BioEdit - Sequence Visualization and Editor software.
  • TreeView - Phylogenetic tree visualization software.
  • Simplot - Recombination software.
Sponsors:
Fogarty ABC Training program:

 Tufts-New England
Medical Center

Africa Centre for Health and Population Studies ABC program

The Nelson R Mandela School of Medicine
Nelson Mandela School of Medicine
The Wellcome Trust


 


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Revised 10th of November 2005 - Copyright @ BioAfrica.