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Generating Multiple Sequence Alignments with ClustalW

Learn how to create multiple sequence alignments using ClustalW, generate phylogenetic trees, and analyze evolutionary relationships among various organisms. Instructions provided for aligning protein sequences of Arabidopsis thaliana RDR6, Schizosaccharomyces pombe Rdp1, Caenorhabditis elegans rrf-2, Caenorhabditis elegans rrf-3, and Aspergillus fumigatus Sad-1. Print out alignments and phylograms to assess relationships.

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Generating Multiple Sequence Alignments with ClustalW

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  1. Generating Multiple Sequence Alignments with ClustalW

  2. ClustalW: creating a multiple sequence alignment • You identify sequences to align • Get Fasta sequences and copy and paste into window or put all sequences in one document and attach (example: copy and paste into one Word document)

  3. ClustalW: Creating the initial alignment

  4. ClustalW: The Alignment Report

  5. ClustalW: The Alignment Report

  6. ClustalW: The Alignment Report

  7. ClustalW: The Alignment Report

  8. ClustalW: Jalview

  9. ClustalW: Jalview

  10. ClustalW: Jalview

  11. ClustalW: creating a phylogenetic tree • ClustalW can only assemble a phylogenetic tree from multiple sequence alignments generated by ClustalW

  12. ClustalW: Making a Phylogenetic Tree

  13. ClustalW: Making a Phylogenetic Tree

  14. ClustalW: Making a Phylogenetic Tree

  15. ClustalW: Making a Phylogenetic Tree Must use Clustal aligned sequences & include “Clustal” line

  16. ClustalW: Making a Phylogenetic Tree

  17. ClustalW: Making a Phylogenetic Tree • Phylogram: tree that provides an estimate of a phylogeny, where the branch lengths are proportional to the amount of evolutionary divergence. • Cladogram: tree that provides an estimate of phylogeny where the branches are of equal length: therefore cladograms indicate common ancestry, but do not reflect amount of evolutionary time separating sequences.

  18. ClustalW: The Phylogram Tree

  19. ClustalW: The Cladogram Tree

  20. ClustalW: Practice Weblem • Align the refseq protein sequences of Arabidopsis thaliana RDR6, • Schizosaccharomyces pombe Rdp1, Caenorhabditis elegans rrf-2, Caenorhabditis elegans rrf-3, and Aspergillus fumigatus Sad-1 using ClustalW. Print out this alignment. • Generate and print out a phylogram and cladogram using this alignment. • Given what you know about the evolutionary relationships between these organisms, does the phylogram and cladogram make sense? Why or why not?

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