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2.1.16.7: Sequence Alignment and Tree Building

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    From LibreTexts, under CC BY-NC-SA 4.0, as the source states it; its equations are written in TeX, which the PDF shows typeset. This page at LibreTexts.

    UGENE

    The following video illustrates the tree-building process using MUSCLE and PhyML in UGENE.

    Command Line

    The following requires:

    • A UNIX-like environment like Linux or MacOS
    • MUSCLE to perform a multiple sequence alignment
    • PhyML to generate Maximum Likelihood
    • FigTree to manipulate the tree

    Download the example file oranges. In the download directory, perform the following:

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    unzip orange.zip

    cd orange

    cat ./*txt >> oranges.fasta ## merges all files into a single fasta file

    muscle -in oranges.fasta -phyiout oranges.phy

    ## -phyiout tells muscle to use the interleaved phylip format for output

    phyml -i oranges.phy -m HKY85

    ## -m is for method and HKY85 is the default nucleotide method we used in UGENE

    mv oranges.phy_phyml_tree.txt oranges.nwk

    ## change the name of the output to reflect it is a nwk file

    This page titled 2.1.16.7: Sequence Alignment and Tree Building was last modified on Mon, 28 Aug 2023 17:40:48 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Shannon Clark.