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    Alignment and Phylogenic Tree Construction Procedures.

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    sewankambosilas

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    Alignment and Phylogenic Tree Construction Procedures.

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    sewankambosilas
    22 views2 pages

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    22 views2 pages

    Alignment and Phylogenic Tree Construction Procedures.

    Uploaded by

    sewankambosilas

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
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    HOW TO ALIGN SEQUENCES AND CONSTRUCT A PHYLOGENETIC TREE

    a. Open the bioedit app. Click on “File”.


    b. Select “New alignment”, in that window, click on sequence, then select new
    sequence, a dialogue box having “Name”, “Sequence type” and space where
    to write the sequences will appear.
    c. Open the folder where your text files with the same primer names are located,
    e.g TR_3_LN20, SR_2_LN20 etc. Open the text document by double clicking on
    it. Select and copy the name of the sequence.
    d. Paste the sequence name in the space which is having “Name” in the dialogue
    box which you opened in bioedit.
    e. In the same text document you opened, select the sequences, copy and paste
    them in the space for sequences.
    f. Click on the drop-down arrow to select the sequence type, “DNA” or “RNA” as
    required.
    g. Repeat procedures b – f up to the required number of sequences.
    h. Click on “file”, then “Save As” to save your work in a folder of your choice.

    To align:
    i. Open the mega app
    j. Click on “File” then select “Open A File/Session”. This will automatically open
    the file explorer.
    k. In the file explorer, find the bioedit file that you saved and open it. A dialogue
    box will appear, select “Align”. Sequences will appear but in a disorganized
    format.
    l. On the tool bar above, select “Alignment” then select “Align by ClustalW”. A
    dialogue box showing that “nothing is selected for alignment” will appear, click
    on “Ok” to select all.
    m. A new window labelled ClustalW options will appear. Here you can use the
    default settings or change the settings of Pairwise and Multiple Alignments as
    instructed then click “Ok”. Wait for a few seconds as the alignment process
    goes on. The sequences will reappear in an aligned format.
    n. Click on “File”, then “Save As” to save your work in a folder of your choice.

    To construct a phylogenetic tree:


    o. In the mega app click on “File” then select “Open A File/Session”. This will
    automatically open the file explorer.
    p. In the file explorer, find the bioedit file that you saved and open it. A dialogue
    box will appear, select “Analyze”. On the dialogue box that appears asking for
    confirmation, click “Yes”
    q. On the tool bar above, click on “Phylogeny” and select “Construct/Test
    Neighbor Joining-Tree…”. In the next window, just click okay. A phylogenetic
    tree will appear.
    r. Click on “File”, then “Save As” to save your work in a folder of your choice.
    Note.
    To be well conversant with the above procedures, get a PC, read as you practice.
    This will help you to explain them in your own words in case of an exam.
    By Engineer Siro aka Child of God the Teacher Pastor Scrap collector.

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