ClustalW Note EBI has retired the ClustalW service see the new presentation Generating Multiple Sequence Alignments with Clustal Omega ClustalW creating a multiple sequence alignment You identify sequences to align ID: 933542
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Slide1
Generating Multiple Sequence Alignments with
ClustalW
Note
: EBI has retired the ClustalW service; see the new presentation "Generating Multiple Sequence Alignments with Clustal Omega"
Slide2ClustalW:
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
Slide3ClustalW: Creating the initial alignment
Slide4ClustalW: The Alignment Report
Slide5ClustalW: The Alignment Report
Slide6ClustalW: The Alignment Report
Slide7Slide8ClustalW: The Alignment Report
Slide9ClustalW: Jalview
Slide10ClustalW: Jalview
Slide11ClustalW: Jalview
Slide12ClustalW:
creating a phylogenetic tree
ClustalW can only assemble a phylogenetic tree from multiple sequence alignments generated by ClustalW
Slide13ClustalW: Making a Phylogenetic Tree
Slide14ClustalW: Making a Phylogenetic Tree
Slide15ClustalW: Making a Phylogenetic Tree
Slide16ClustalW: Making a Phylogenetic Tree
Must use Clustal aligned sequences
& include “Clustal” line
Slide17ClustalW: Making a Phylogenetic Tree
Slide18ClustalW: 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.
Slide19ClustalW: The Phylogram Tree
Slide20ClustalW: The Cladogram Tree
Slide21ClustalW: 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?