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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> DNA data-taxon names http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1176250549 Message started by jxn on Apr 10^th, 2007 at 5:15pm

Title: DNA data-taxon names
Post by jxn on Apr 10^th, 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

Title: Re: DNA data-taxon names
Post by Sergei on Apr 10^th, 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)))))
[/code]

Cheers,
Sergei

Title: Re: DNA data-taxon names
Post by jxn on Apr 11^th, 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

Title: Re: DNA data-taxon names
Post by Sergei on Apr 11^th, 2007 at 12:45pm

Dear jxn,

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

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