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Generating Multiple Sequence Alignments with ClustalW

Generating Multiple Sequence Alignments with ClustalW. 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).

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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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