Version 1.2
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    • Sequence Alignment with the Selected Reference Sequence
    User input sequences will be aligned against the corresponding K12 reference sequence using the computer program CLUSTAL W (version 1.83). If a K12 reference sequence is not specified by selecting an allele name, user input sequences will be aligned against each other. The phylogenetic tree generated can be displayed by ATV. The alignment can be displayed by the Jalview multiple alignment editor.

    Step 1: Select the reference allele. Leave it as null if the reference sequence is not needed for the alignment.


    Step 2: DNA sequence(s) in FASTA format


    Step 3: Select an alignment algorithm, then set the related parameters
    Fast pairwise alignment
    Gap penalty
    		 Word size
    		 Top diagonals
    		 Window length
    		 Score
    Slow pairwise alignment
    Open gap
    		 Extend gap
    		 Weight matrix
    Multiple alignment
    Open gap
    		 Extend gap
    		 Weight matrix
    Delay divergent sequences
    		 Transition weight

    Step 4: Alignment output
    Output format
    		 Output order

    Step 5: Phylogenetic tree output
    Output tree
    		 Correct distance
    		 Ignore gaps
        
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    Operated by the Microbial Evolution Laboratory at Michigan State University
    National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (NIAID) Food and Waterborne Diseases Integrated Research Network (FWD IRN) Microbiology Research Unit (MRU) Reference Center to Facilitate the Study of Shiga Toxin-Producing Escherichia Coli