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DNA data-taxon names (Read 3851 times)
jxn
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DNA data-taxon names
Apr 10th, 2007 at 5:15pm
 
hi, i kept having the error message about the data

The leaf of the tree:myTree labeled Node1 had no match in the data. Please make sure that all leaf names correspond to a sequence name in the data file.

my code:
Tree myTree = (Or((Mc,Gb)(Hm(Gr(Ch,Bo)))));

my data is in .txt file, the leaf names are Or, Mc,etc

Do I need any specific struture of the data?can it be .txt? or must be .seq?

Should the species name start with #?seperate with the ACGT by space?

Thank you so much
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Sergei
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Re: DNA data-taxon names
Reply #1 - Apr 10th, 2007 at 5:43pm
 
Dear jxn,

Your tree is not defined properly (seems like you are using PAML like syntax - it is non-standard and should be avoided).

Define the tree using the standard Newick format (using commas to separate siblings, regardless of whether or not they are leaves or internal nodes):

Code:
(Or,((Mc,Gb),(Hm,(Gr,(Ch,Bo)))))
 



Cheers,
Sergei
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jxn
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Re: DNA data-taxon names
Reply #2 - Apr 11th, 2007 at 9:51am
 
Hi, Sergei

I changed the tree defined to

(Or,((Mc,Gb),(Hm,(Gr,(Ch,Bo)))))

Error:The number of tree tips in myTree (7) is not equal to the number of species in the data filter associated with the tree (0).

the data file is 7 species, start with species name, then sequence. does the data file need a special format?

Thanks

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Sergei
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Re: DNA data-taxon names
Reply #3 - Apr 11th, 2007 at 12:45pm
 
Dear jxn,

Here's the description of data formats that HyPhy understands:

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Cheers,
Sergei
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Division of Biomedical Informatics
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