Re: [Dart-help] [Fwd: xrate and visualizeRates.pl]

[Robert B. <rbr...@be...>]

Hi Jakob,
I've cc'ed the dart-help mailing list.  If you like, you can subscribe  
to the low-volume lists dart-help (https://lists.sourceforge.net/lists/listinfo/dart-help 
) and dart-announce (https://lists.sourceforge.net/lists/listinfo/dart-announce 
).

The fault was mine with HKY85--a bug with the (simplest!) case where  
there is only one Markov chain in the grammar.  You can get the bugfix  
with a cvs up of your copy of dart.  Please let me know if you're  
still having problems.

Perhaps you've already found these pages, but http://biowiki.org/XrateSoftware 
  gives some information about Xrate and http://biowiki.org/ 
XrateFormat information about the Xrate grammar format and its rapidly- 
expanding capabilities.

I hope that you enjoy using this software!

take care,
Rob

On Feb 1, 2008, at 6:37 AM, Jakob Skou Pedersen wrote:

> Dear Robert,
>
> Many thanks for your detailed and prompt reply. Esteban was just  
> helping for a brief spell and I will probably be the one bothering  
> you with any questions in the future.
>
> I successfully ran visualizeRates.pl on several of the examples  
> provided. However, I could not get it to run on the single- 
> nucleotide matrices (e.g., HKY). However, I only tried it briefly  
> and will return to you if the problems persist after having tested  
> it more thoroughly.
>
> I love the program and think it is extremely neat and helpful!
>
> Cheers,
> Jakob
>
>
>
> On Jan 31, 2008, at 6:56 PM, Robert Bradley wrote:
>
>> Hello,
>> I can probably help you out with this.  I'm a grad student in the  
>> Holmes lab and I wrote a lot of the visualizeRates code.  You can  
>> see a short description at http://biowiki.org/BubblePlots.
>>
>> There are lots of sample grammars in dart/grammars/.  You can test  
>> out the bubbleplots as e.g.
>> /usr/local/dart/perl/visualizeRates.pl /usr/local/dart/grammars/ 
>> codon.eg
>> (replacing '/usr/local/dart' with your dart install directory).
>>
>> The most common error which people have is due to not having the  
>> required dart perl libraries accessible.  You can add a line to  
>> your .bashrc file to fix this:
>> export PERL5LIB=/usr/local/dart/perl:$PERL5LIB
>> and similarly for tcsh, etc.
>>
>> Does this help?  If you're still having problems, please don't  
>> hesitate to ask.
>>
>> Rob
>>
>>> From: Esteban Czwan <cz...@bi...>
>>> Date: January 31, 2008 2:20:30 AM PST
>>> To: ybe...@be..., bi...@ar...
>>> Cc: ih...@be..., Jakob Skou Pedersen <js...@bi...>
>>> Subject: xrate and visualizeRates.pl
>>>
>>>
>>> Dear Yuri and Mitch,
>>> I'm assisting Jakob Pedersen in teaching a course in  
>>> "phylogenetics and comparative genomics" this quarter and he would  
>>> love to use xrate. The plan is to let the students use it to  
>>> estimate rate matrices from different genomic regions, visualize  
>>> them as bubble plots, and do some interpretation. Later in the  
>>> course he would also like to have them construct some simple phylo- 
>>> HMMs / phylo-grammars.
>>>
>>> I believe I have managed to use xrate to estimate a rate matrix  
>>> but I can't get the bubble plot script to work on the grammar file  
>>> trained. I always get the same error:
>>> "Can't call method "find_all" on an undefined value at ChainDat.pm  
>>> line 141."
>>> For that matter, I get the same error on any grammar file that I  
>>> use as input. Most likely, I am doing something totally wrong. Do  
>>> you happen to have any student exercises / examples / tutorials on  
>>> xrate that you can share with us?
>>> I have looked at http://biowiki.org/XrateSoftware but I didn't see  
>>> any of those.
>>>
>>> Many thanks!
>>>
>>> Best,
>>>
>>> -Esteban
>>>
>>> cc:
>>> Jakob P.
>>> Ian H.
>>>
>>>
>>
>