I succeeded to run SingleBreakpointRecomb.bf from GUI based on page 52 in 'hyphybook2007.pdf', but I still don't figure out how to run this analysis from a command-line. Can HYPHY GUI Console print the command-line description for this analysis?. Which documents should I read to familiar with it?

I cannot fine $HYPHYMP executable file in the HYPHY folder (Mac OS X Universal Binary) although 'README' states 'HYPHYMP (Multiprocessor)'. Where is it available? Thank you

(1)
For v1.0 release, 'bash build.sh MP2' succeeded to produce HYPHYMP.
For v2.0 developmental build, 'bash buildFromSVN.sh' failed and printed the following messages:
##########
cc1plus: error: unrecognized command line option "-fopenmp"
Error during compilation
Darwin
gtk_build.sh: line 20: pkg-config: command not found
##########

(2)
Running
'./HYPHYMP BASEPATH=. TemplateBatchFiles/SingleBreakpointRecomb.bf' where current directory (.) is 'HYPHY_Source'
printed './TemplateBatchFiles/Locate a nucleotide data  file::'
Then, input data file 'InfluenzaA_H3_Random35.nex' located at current directory printed as follows:
##########
./TemplateBatchFiles/Locate a nucleotide data  file::InfluenzaA_H3_Random35.nex
Error:
Could not find source dataset file:PROMPT_FOR_FILE Path stack: {/Users/hs/HYPHY_Source/,./TemplateBatchFiles/}
Current BL Command:Read Data Set ds from file PROMPT_FOR_FILE

Check errors.log for details on execution errors.

Check messages.log details of this run.
##########
Why should data file be located at not current directory (.) but 'TemplateBatchFiles' directory?

Hello

(1)
For v2.0, when I edit the 'build.sh' file (COMPILER="g++-4.2"; COMPILERC="gcc-4.2", 'bash buildFromSVN.sh' succeeded to produce HYPHYMP, although it still printed the following messages:
##########
gtk_build.sh: line 20: pkg-config: command not found
*snip*
cc1plus: error: unrecognized command line option "-fopenmp"
Error during compilation
##########

(2)
The following command-line descriptions with absolute path successfully finished.
mydir=/Users/$USER/hyphy/HYPHY
$mydir/HYPHYMP BASEPATH=$mydir $mydir/TemplateBatchFiles/SingleBreakpointRecomb.bf < answers.txt >& stdout.txt
where the 'answers.txt' file contains:
##########
1
/Users/$USER/InfluenzaA_H3_Random35.nex
1
CUSTOM
012212
2
1
1
output.txt
##########
Although $PWD=/Users/$USER and BASEPATH=/Users/$USER/hyphy/HYPHY, it still printed
'/Users/$USER/hyphy/HYPHY/TemplateBatchFiles/Locate a nucleotide data  file::'
'/Users/$USER/hyphy/HYPHY/TemplateBatchFiles/Save results to::'

(3)
After installing from Source (v2.0), SingleBreakpointRecomb.bf from GUI (Mac OS X Universal Binary) cannot progress after typing 'Please enter a 6 character model designation (e.g:010010 defines HKY85):012212'

Thank you,

I used GUI version (Mac OS X Universal Binary) to implement SingleBreakpointRecomb.bf. After selecting 'CUSTOM' and then [OK] in 'Choose one of the standard models' window, HYPHY Console printed 'Please enter a 6 character model designation (e.g:010010 defines HKY85):'. Then, I typed 012212 and [enter] but nothing happened.
A GUI version (Mac OS X) and command line version (v2.0) are incompatible, and installing both version can cause this problem?

When I typed 012212 in the lower part (entry box) of the console window, it worked well. Thank you.

I run SBP on '12.phy' from different HyPhy versions.
(1) command line version (Source v2.0 developmental build Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) on Mac OS X (10.5.8) succeeded.
(2) command line version (C/C++ Source. Linux/gcc Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) on x86_64 GNU/Linux failed, and printed the following error messages in 'messages.log'.
Row and/or column partition is empty. All the data will be used by default.Incompatible Matrix Dimensions Exiting...
Current BL Command:totalSitesCompared=Transpose(summingVector)*(siteDifferenceCount*summing
Vector)
(3) GUI version (Mac OS X Universal Binary) on Mac OS X (10.5.8) also failed, and printed the error messages.

(3) is also outdated..

[Questions]
(i) In most alignments analyzed, SBP detected breakpoints based on AIC and AIC-c, while no recombination based on BIC. Would you use BIC to judge presence of recombination in alignments?
(ii) SBP may be affected by the number of sequences in alignments? (alignments must include at least four sequences to detect phylogenetic incongruence)
(iii) SBP may falsely detect recombination due to the presence of positive selection?

[References]
(i)
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BIC was selected because it had the best power/accuracy performance in our initial simulation studies, comparing AIC [36], AIC-c [37] and BIC
(ii)
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We noticed that when samples were reduced, the GARD algorithm found a significantly higher number of recombination breakpoints. For example, in the nef gene of HIV-2, when 24 sequences were used, only one breakpoint was inferred. When downsized to 10 sequences, four breakpoints were estimated.
(iii)
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We note that large scale surveys for recombination using traditional detection software [e.g., [22]] are possible, but such programs likely suffer from an inverse effect, i.e. recombination may be falsely detected due to the presence of positive selection.

SBP can perform SH testing? If not, I would select 'KH Testing' (Run 1 or 2). How many KH samples should be drawn per breakpoint?