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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> NJtree.TG is already been used http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1130235399 Message started by Antonio on Oct 25^th, 2005 at 3:16am

Title: NJtree.TG is already been used
Post by Antonio on Oct 25^th, 2005 at 3:16am

hi, I am getting an strange crash since I am doing something I think I done before without problems ???.

Whith MoleculaClock.bf or whenever I open a tree file I get a message as "NJtree.TG is already being used- please rename one of these two variables". I get the same message when I compute a NJtree and try to store it programatically, that is: the same message as before, plus "Current BL comman:d Build NJTree from String mytreeString...

Sincerely,
Antonio

Title: Re: NJtree.TG is already been used
Post by Sergei on Oct 25^th, 2005 at 7:10am

Dear Antonio,

Check for '.' (or other non-alphanumerics) in sequence names and replace them with underscores. If that is not the issue, then I may have to see the data file to replicate the error.

Cheers,
Sergei

Title: Re: NJtree.TG is already been used
Post by Antonio on Oct 25^th, 2005 at 8:11am

Thankyou very much, it was my fault, there was one file with bad format somewhere.
,
antonio

Title: Re: NJtree.TG is already been used
Post by Sarah on Aug 29^th, 2006 at 11:08am

I'm having a similar problem, but I can't find an error in my tree file. Does HyPhy not tolerate prespecified branch lengths?

Thanks for the help.

Title: Re: NJtree.TG is already been used
Post by Sergei on Aug 29^th, 2006 at 11:23am

Dear Sarah,

HyPhy will read branch lengths, provided they are properly formed numbers. I'll be happy to take a look at your tree (just e-mail it to me as an attachment) and see if I can find what the problem is.

Cheers,
Sergei

Title: Re: NJtree.TG is already been used
Post by Sarah on Aug 30^th, 2006 at 7:03am

<doh> Not enough coffee yesterday--I think the problem might be the bootstrap values in all my Newick files. HyPhy doesn't tolerate them, right?

Thank you for the help.

Sarah

Title: Re: NJtree.TG is already been used
Post by Sergei on Aug 30^th, 2006 at 7:33am

Dear Sarah,

wrote on Aug 30^th, 2006 at 7:03am:

<doh> Not enough coffee yesterday--I think the problem might be the bootstrap values in all my Newick files. HyPhy doesn't tolerate them, right?

Depends on how they are specified. Could you paste in a short fragment of the tree?

Cheers,
Sergei

Title: Re: NJtree.TG is already been used
Post by Sarah on Aug 30^th, 2006 at 7:59am

Here's a small fragment I copied directly from the end--the parentheses don't match:

(5HK6869:0.00517100,4HK6868:0.01945300)36:0.00108000)22:0.00000000,13HK6871:0.01482200)62:0.00206400,(6HK6869:0.00103300,((9HK6870:0.00312700,8HK6870:0.00418200)69:0.00102000,7HK6869:0.00103400)54:0.00103400)71:0.00206900)94:0.00000000,3HK6868:0.00000000,2HK6868:0.00000000);

The tree is the output from a PHYML run with 100 bootstraps. My sequence names are all alphanumerics <=10 characters long.

Sarah

Title: Re: NJtree.TG is already been used
Post by Sergei on Aug 30^th, 2006 at 8:14am

Dear Sarah,

Sequence names and branch lengths are fine, but HyPhy will interpret bootstrap support for internal branches as branch names (e.g. ...13HK6871:0.01482200)62 will give the parent of 13HK6871 the name '62'). If any two internal branches have the same BS support, you'll run into the 'duplicate name' issue.

Cheers,
Sergei

Title: Re: NJtree.TG is already been used
Post by Sarah on Aug 30^th, 2006 at 8:16am

Thank you!

I will remove the bootstrap values, then (assuming there's no way to tag them so HyPhy read/ignores them).

I really appreciate the help.

Sarah