Dear All,

This is my first brush with HyPhy but I am amazed at the number of citations that HyPhy has got, even though this package is quite young.
I just installed HyPhy on my Red hat machine and am a novice with HyPhy, to say the least.

What I want is to run HyPhy on my alignment file and see if there is some added constraint on the sequences in the alignment, in addition to the ones for protein coding. This essentially means that for some regions (which have regulatory purpose, like splicing enhancers), I should see a reduced synonymous site variation, or reduced synonymous rate.
So I launch HyPhy from my terminal, and I get a menu from where I could select the analyses. I think for my current problem, I should select #14 (Substitution Rates). When I type 14, I get a prompt, "Please select type of analyses you want to list (or press ENTER to process custom batch file)". I specify the path of my alignment then, but it just does not seem to work from here on.
I may be asking very stupid questions, but any feedback on my line of thinking as well as technical help will be more than welcome

Regards

Hi there,

You will probably find the following two book chapters useful introductions to HyPhy and selective analyses. HyPhy has grown to be a very complicated and somewhat intimidating beast, so please let me know if you need more specific guidance.

Sergei

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Dear Sergei,
Thank you very much for pointing me to the relevant literature.
However, I have a few problems in configuring Hyphy on my 8-core linux machine. What I did was the following:

1) Made a directory hyphy.
2) cd to hyphy
3) svn checkout "the website URL" (cannot post it here)
4) cd to /home/DATA/hyphy/trunk/Scripts
5) buildFromSVN.sh /home/DATA/hyphy/HYPHY
6) cd to /home/DATA/hyphy/HYPHY
7) bash build.sh MPI

However there are errors and I am reproducing the output below


bash build.sh MPI
Linux
Checking for curl
curl_check.cpp:1:23: error: curl/curl.h: No such file or directory
Curl seems to be absent (setting up compiler options skip CURL code)
+-----------------------------------------------------------+
|Building a single-threaded HYPHYKernelMPI for MPI          |
+-----------------------------------------------------------+
COMPILER=g++, gcc
COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive -I/home/DATA/Virag/hyphy/HYPHY/Source -I/home/DATA/Virag/hyphy/HYPHY/Source/SQLite -D INTPTR_TYPE=long -D __UNIX__  -D _SLKP_LFENGINE_REWRITE_  -D__HYPHY_NO_CURL__ -D __HYPHYMPI__ -D _SLKP_LFENGINE_REWRITE_
Building baseobj.cpp
In file included from baseobj.cpp:34:
batchlan.h:395:18: error: mpi.h: No such file or directory
baseobj.cpp: In function âbool GlobalShutdown()â:
baseobj.cpp:244: error: âMPI_COMM_WORLDâ was not declared in this scope
baseobj.cpp:244: error: âMPI_Comm_sizeâ was not declared in this scope
baseobj.cpp:264: error: âMPI_Finalizeâ was not declared in this scope
Error during compilation


Could you advise me on this error please ?

Regards

Hi there,

Please take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for some suggestions.

Best,
Sergei