You can also use sturcture (Pritchard et al, Genetics 2000).

Dear Dr Andrew King, thank you for the feedback. I am currently also using STRUCTURE, but can we confidently infer the stages of hybridization based on STRUCTURE clustering results?

You can also use the adegenet package

http://adegenet.r-forge.r-project.org/

Hindex is a good alternative to NewHybrids. This program assigns a value (index) between 0 (parent 1) and 1 (parent 2) to each individual using a maximum likelihood approach. So an F1 would be somewhere around 0.5. 95% CI for each index are given as well. Unfortunately there's only a Mac version for this software. Here's the link

http://www.uwyo.edu/buerkle/hindex/

Hi Dr Wei, I am also looking for a way to discriminate the hybrid status with Structure software. I found some one did it (POLLINATOR-MEDIATED REPRODUCTIVE ISOLATION AMONG DIOECIOUS FIG SPECIES (FICUS, MORACEAE) http://dx.doi.org/10.1111/j.1558-5646.2012.01727.x). They calculated the posterior probabilities of the F1, F2 and no-hybrid individual that should be you wanted. However, I  couldn't get that result form with described method. I hope you can get it and share with us. Thanks.

Hi Dr Wei, did you finally work with NewHybrids software? I would appreciate to contact you to ask some questions about it. Thanks!

Hi Ana,

Yes I used the NewHybrids software in my recent publication, and I was running the Mac version. However, I still could not generate the graph with NewHybrids, just the posterior probability values in each generation group (Px, Py, F1, F2, Bx, By). Then I plotted the values into a graph on Excel. You can refer to my publication and the accompanying supplementary data for a better idea:

http://www.sciencedirect.com/science/article/pii/S0304377014001107

Hope it helps.

Wei Lun

Would you mind if I e-mail you to ask some questions about your analysis? Already read your paper and I think my data set might present a similar situation.

Thanks!

Ana

Dear Dr Wei Lung Ng 

we have tried to use the program Newhybrids and we could not.

We put the glut32.dll file in the same folder of the program. In Windows the program opens, but when we try to use the program it crashes in the graphical interphase option.

Without the graphical interphase we can continue a little bit more; after setting the burnin and the number of iterations after that period, the program crashes with the following message:  

unhandled exception: c0000005

At adress:  0040b097

We also tried to install the OpenGl v1.1 software but we couldn't.

We tried  all the procedure in a Windows7-64bits computer and in a windowXP-32bits computer.

We follow the instructions of the program, but it doesn´t work

Could you please help us?

Thank you very much.

Dr. Gonzalez-Ittig

Dear Dr. González-Ittig,

I am using NewHybrids and I am also getting that unhandled exception.

I've tried different things (cutting out alleles or genotypes) and sometimes I make it work and sometimes not in a complete random fashion.

Did you figure out what is the source of the problem?

I am also having the message of unhandeled exception. Anyone who have experienced and solved this problem.

Dear colleaques,

I tried to run NewHybrids having the input comrosing 318 individuals and almost 2000 AFLP loci. It didn't work and "unhandled exception" was shown. Without any problem I conducted analyses with the "parallelnewhybrid" by Wringe et al. (2017, Molecular Ecology Resources).

Hello everyone! Thank you for your answers. I have the same problem and I have already deleted specimens with missing alleles. Burnin goes good but when it starts sweeps after burnin it fails with mentioned error :(

Check your inputfile

Input file works good with 4 loci but with 3 loci newhybrids interrupts sweeps after burning

I too have been having trouble running NewHybrids. I am running the WOG beta version. About 4 days ago, I had a successful run with 795 individuals and 33 microsatellite loci, 100,000 burnin followed by 500,000 iterations. When I tried to run it a second time with a dataset simulated in Hybridlab, the run failed during burnin. Now, no matter the input file (e.g., the same file that ran successfully or the testdata files that came with the NewHybrids software) I get the same exception error message as mentioned above. I suspect accumulated crossed-wires between the operating system and the software. Is that possible? Does anyone have suggestions as to how to fix that? The software does work.

I am having similar problems with NewHybrids on Windows (also using the WOB beta version) as Maria and Shauna have described. Msat data loads correctly, burnin finishes, but MCMC iterations only proceed through 1,000-3,000 ish sweeps prior to "Unhandled exception" error message. At first I suspected RAM limitations, but now think it may be a software / operating system compatibility issue. I'm going to try to get things to run in the R package "parallelnewhybrids" available on GitHub.

For those with access to a Mac with OSX, the following may be helpful, as it appears the Mac version is updated more often. I was able to get NewHybrids (without graphics) to run reliably using the steps below. Note that I'm no programming expert, so there may be easier ways, but this worked well for me after trudging through available documentation online. Hopefully this saves someone some hours of agony.

1) Download and extract all files from GitHub site: github.com/eriqande/newhybrids

2) Follow folders system to Bin -> OSX -> newhybridsng.exec (run this; no graphics version)

3) Back at the main folder downloaded from GitHub, open a new Terminal Window at this folder location (can be done on some machines by right-clicking the main folder)

4) Copy and past the following into the terminal to see a helpfile of all available commands: ./bin/OSX/newhybsng --help-full

5) Using this documentation, string together necessary analysis of desired datafile. Note that "--no-gui" command is needed at end to make the "no graphics" version work. The below example loads the test data file "TestDat.txt" that comes with NewHybrids, along with personalized model specifications. Also note that your data files are likely stored in a different location, but you may be able to drag-and-drop the data file into your Terminal window to obtain the file path needed.

Example Terminal command: ./bin/OSX/newhybsng --datafile /Users/Andrew/Desktop/newhybrids-master/test_data/TestDat.txt --theta-prior uniform --pi-prior uniform --burn-in 50000 --num-sweeps 100000 --no-gui