08/14/2020 1 Generating Multiple Sequence Alignments with ClustalW Note: EBI has retired the ClustalW service; see the new presentation "Generating Multiple Sequence Alignments with Clustal Omega" 1 ClustalW: creating a multiple sequence alignment • You identify sequences to align • Get Fasta sequences and copy and paste into the ClustalW window (see next slide) • Alternatively, put all the sequences into one plain text document (e.g., using WordPad on Windows, TextEdit on macOS) and save the file • Click on the “Browse” or “Choose File” button under the “Enter your input sequences” section and select the file 2 ClustalW: Creating the initial alignment 3 ClustalW: The Alignment Report 4 ClustalW: The Alignment Report 5 ClustalW: The Alignment Report 6
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08/14/2020
1
Generating Multiple Sequence Alignments with ClustalW
Note: EBI has retired the ClustalW service; see the new presentation
"Generating Multiple Sequence Alignments with Clustal Omega"
1
ClustalW: creating a multiple sequence alignment
• You identify sequences to align
• Get Fasta sequences and copy and paste into the ClustalWwindow (see next slide)
• Alternatively, put all the sequences into one plain text document (e.g., using WordPad on Windows, TextEdit on macOS) and save the file• Click on the “Browse” or “Choose File” button under the
“Enter your input sequences” section and select the file
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ClustalW: Creating the initial alignment
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ClustalW: The Alignment Report
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ClustalW: The Alignment Report
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ClustalW: The Alignment Report
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ClustalW: The Alignment Report
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ClustalW: Jalview
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ClustalW: Jalview
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ClustalW: Jalview
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ClustalW: creating a phylogenetic tree
• ClustalW can only assemble a phylogenetic tree from multiple sequence alignments generated by ClustalW
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ClustalW: Making a Phylogenetic Tree
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ClustalW: Making a Phylogenetic Tree
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ClustalW: Making a Phylogenetic Tree
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ClustalW: Making a Phylogenetic Tree
Must use Clustal aligned sequences& include “Clustal” line
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ClustalW: Making a Phylogenetic Tree
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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.
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ClustalW: The Phylogram Tree
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ClustalW: The Cladogram Tree
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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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