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Thread: phylogenetic program that can analyze ambiguity codes

  1. #1 phylogenetic program that can analyze ambiguity codes 
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    systematicists and phylo gurus,

    i am looking for a phylogenetics program that can produce a tree using consensus sequences (dna) that have ambiguity codes (IUPAC codes for multiple bases such as R, K, Y, W, and so on). so far, dnapars/fdnapars is the only one i have stumbled across, but i am not very excited about going the parsimony route. anything bayesian, or at the least, ML-related would be ideal.

    your help is much appreciated. thanks


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  3. #2 Re: phylogenetic program that can analyze ambiguity codes 
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    Quote Originally Posted by bhikhaari
    systematicists and phylo gurus,

    i am looking for a phylogenetics program that can produce a tree using consensus sequences (dna) that have ambiguity codes (IUPAC codes for multiple bases such as R, K, Y, W, and so on). so far, dnapars/fdnapars is the only one i have stumbled across, but i am not very excited about going the parsimony route. anything bayesian, or at the least, ML-related would be ideal.

    your help is much appreciated. thanks
    BEAUTI/BEAST is a good package. Not sure if it analyses DNA (one would think any package would have this functionality) but is solid bayesian package and superior to most other analysis I have seen.

    Otheriwise, common tools include geneiuos, clustal (any such) and you might check out phylogeny.fr. as this site always has links that surprise me.

    http://www.phylogeny.fr/

    best bet:

    http://beast.bio.ed.ac.uk/Main_Page


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