What This Document Is
This is a laboratory exercise designed to accompany a course on phylogenetic principles and systematics. It focuses on the practical application of sequence alignment techniques – a crucial step in building evolutionary trees. The lab explores how different computational approaches and parameter settings impact the resulting alignments, and ultimately, phylogenetic interpretations. It’s a hands-on guide intended to reinforce theoretical concepts with practical experience.
Why This Document Matters
This resource is ideal for students enrolled in courses covering phylogenetics, evolutionary biology, bioinformatics, or molecular systematics. It’s particularly valuable when you’re learning to analyze molecular data and understand the complexities of multiple sequence alignment. If you’re preparing to undertake a research project involving phylogenetic analysis, or simply want to deepen your understanding of how alignment choices influence results, this lab will provide a solid foundation. Accessing the full content will allow you to actively engage with the material and develop essential skills.
Topics Covered
* Multiple Sequence Alignment methodologies
* The impact of alignment parameters on phylogenetic inference
* Using ClustalW for sequence alignment
* Converting alignment file formats (e.g., FASTA to Nexus)
* Introduction to POY – a combined alignment and tree searching program
* Evaluating alignment quality and interpreting alignment scores
* Practical considerations for large datasets and computational efficiency
What This Document Provides
* Guidance on obtaining sequence data from public databases.
* Detailed instructions on accessing and utilizing online bioinformatics tools.
* A framework for comparing different alignment strategies.
* Information on interpreting output files generated by alignment software.
* A practical exercise designed to illustrate the effects of parameter choices on alignment results.
* Contextual information relating alignment choices to broader phylogenetic analyses.