prealigned

[ajj...@gmail.com]

Is this script possible?

read(prealigned:(aminoacids:("xxx.fas"),tcm(1,1)))

I have an error

thanks you

Adrian

[Louise Crowley]

Hi Adrian, 

First of all, this script is incorrect—a colon needs to follow the tcm:

read(prealigned:(aminoacids:(“xxx.fas”),tcm:(1,1)))

However, there is a problem with reading in prealigned amino acids files with the current version of POY5.  This bug has been fixed, and will be available in the next release of POY5.

In the meantime, if you tell me the operating system that you are working with, we can compile binaries for you to work with.

Best, 

Louise

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[Louise Crowley]

Hi All, 

Actually, the issue that I mentioned in my previous reply was with reading prealigned nucleotides and not aminoacids.

However, the error below still relates to the absence of the colon after the tcm.

For those of you wishing to read in prealigned nucleotides, a POY5 version [5.1.2], is available on the POY google codes website https://code.google.com/p/poy/

Best, 

Louise

On Jun 29, 2014, at 8:26 PM, ajj...@gmail.com wrote:

[Leonardo Borges]

Louise, I could not find the link for POY 5.1.2 at the page.

Unless I am looking at the wrong place, there are only files for version 5.1.1.

Thanks,

Leonardo

aquitemcaqui.com

[Nicholas Lucaroni]

That's right, I only updated the source. We can make binaries, but check the changes and see if they are important to you. The changes are a minor syntax change as Louise mentioned, a clarification of the clear_memory command, and a memory intensive parallel fuse ( with the 'all' option passed ).

I also did minor work in improving the optimization of models and branches for MPL likelihood, but more effort needs to be done.

Nick

[Leonardo Borges]

Nick, I was indeed looking for the source code in the hope to load prealigned datasets without problems.

All files in the download page, however, are labeled 5.1.1, including the source.

Leonardo

aquitemcaqui.com

[Nicholas Lucaroni]

Good call. I forgot about the packaged source code. The source I had meant is through the mercurial connection provided by Google code. The information is provided on this page,

https://code.google.com/p/poy/source/checkout