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  • Bootstrapping in Neighbor (Phylip package)

    Hi,

    I am very new to phylogenetics. I have to construct Phylogenetic tree from SNP Golden Gate data. I generated distance matrix and used "Neighbor" of Phylip package. I am not sure how do I use bootstrapping there? Do I really need to do bootstrapping or the tree generated as it is I can use.trust.

    Thanks
    Neha

  • #2
    Wow. I have to take pieces of memmory I though they would be lost!

    Once you have dist-neighbor analysis, reuse your initial dataset as input for bootseq (bootstrap/jacknife), do the boostraping and then use that output for dnadist-neighbor-consense. So basically you will have x (# bootstraps) alignments, x distance matrix, x trees.
    ....more or less
    Last edited by cascoamarillo; 03-19-2015, 09:48 AM.

    Comment


    • #3
      and remember to use the Multiple data sets option (M) to analyze them all

      Comment

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