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HYPHY Package >> Feature Additions >> [ADDITION] Batch genome analysis
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Message started by Sergei on Feb 7th, 2007 at 4:02pm

Title: [ADDITION] Batch genome analysis
Post by Sergei on Feb 7th, 2007 at 4:02pm
Greetings,

I am starting to put together a library of codon based analyses aimed at batch processing of many alignments of orthologs (e.g. for gene-by-gene genome comparison).

Here's something to start this going (take a look at the README file)

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I especially welcome suggestions on what would be useful to have here.

Cheers,
Sergei




Title: Re: [ADDITION] Batch genome analysis
Post by Mike on Sep 20th, 2007 at 3:20am
Hi Sergei - this looks like just the kind of analysis that I need to do.  Have you continued to develop this since you posted the message in Feb?  If you have more recent code I will be happy to try it out.
cheers
Mike

Title: Re: [ADDITION] Batch genome analysis
Post by Sergei on Sep 20th, 2007 at 6:52am
Dear Mike,


wrote on Sep 20th, 2007 at 3:20am:
Hi Sergei - this looks like just the kind of analysis that I need to do.  Have you continued to develop this since you posted the message in Feb?  If you have more recent code I will be happy to try it out.
cheers
Mike


I have streamlined the code and written documentation on how to develop new modules, but I haven't added more modules. The whole pipeline is being integrated into the Galaxy data analysis framework, developed at Penn State U, so eventually there should be quite a few. I updated the original link with the latest files.

Cheers,
Sergei

Title: Re: [ADDITION] Batch genome analysis
Post by sergios-orestis on Apr 20th, 2012 at 5:47pm
Dear Sergei,

I was wondering if you had revised/updated GenomeFitters since that 2007 post or if there is another bf we could use. I would like very much to scan for positively selected codons individual alignments (thousands of them) from bacterial NGS data.

Any advice is most welcome, as always.

Best,
Sergios

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