Anonymous posted a comment on discussion BayesAss Q&A

Thank you for responding. I see. But it is only rough estimation. I want to know the detail value. Can I extract the MCMC's distribution of m ?

Anonymous posted a comment on discussion BayesAss Q&A

Hi all, I have been using BayesAss to investigate recent migration between 2 populations with a low pairwise Fst of 0.0046. There are no issues with acceptance rates and over 10 runs I've been getting very consistent migration estimates, virtually identical to the result below: m[0][0]: 0.9904(0.0074) m[0][1]: 0.0096(0.0074) m[1][0]: 0.3205(0.0094) m[1][1]: 0.6795(0.0094) The migration rate standard deviations for the 2 populations over the 10 runs are 0.00032015 and 0.000240832. Based on the above,...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I've got a question about the SNP vs. microsat executables of this version. I've run BA3Win64MSAT with microsat data on my PC and that runs fine. I've then had BA3X86_64 installed on our cluster, and tried to run the same microsat data (after taking care of 'Windows' issues by changing the infile in Ubuntu). The cluster version runs fine with the example file (2pop.txt which is SNP data). My own run starts normally, correctly reports the loci, but then gives a "Segmentation fault". Does this...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, Regardless of how I change the delta values or seed, I get a migration rate of 0 for all comparisons. My trace file is also empty, which suggests to me that something is wrong. My populations have very low structure, so I wonder if this could be why? Does anyone have any advice? Cheers, Lily

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I am using BayesAss for 8 populations and 33 microsatellite loci. The mixing parameters for migration rate, allele frequency and inbreeding coeff meet the acceptance rate, but the individual migrant ancestry is always very low (0.00 or 0.01). When looking at the output files, the results don’t seem consistent between migration rates and individual ancestry. When I look at the trace file, my run seems to have converged. Can I adjust the parameters for the individual migrant ancestry too? Or else...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I am trying to use Bayesass 3.04 with msat data, but it says it can't open the file and I don't know why. I attach the input file I'm using. Fernando

Anonymous posted a comment on discussion BayesAss Q&A

I am using v 3.04 with microsat data. I am not 100% clear on how to interpret the prior densities vs the posterier. Most of the time in the literature I don't seen anything written about comparisons to the priors, especially if the newest verision of BayesAss was used. But when people do compare to the priors, I have seen it discussed in 2 different ways and it is not clear to me which is more correct (or appropriate): 1) the CI's with the 'real' data do or do not overlap with the prior CIs - if...

Anonymous posted a comment on discussion BayesAss Q&A

I are very interested in using BAYESASS in order to estimate migration rate between populations. However, when we use the command: C:\Users\MAGP\Desktop\BA3Windows64\BA3.exe -v examples\3pop.txt we obtain the following error mensaje. error: cannot open file: 3pop.txt quitting... Could you help me with this?

Anonymous posted a comment on discussion BayesAss Q&A

Hi everybody, I have detected hybrids between two species using NEWHYBRIDS software, which is in agreement with STRUCTURE results. However, Bayesass detected low migration rates between populations (0.01 - 0.07). How could I explain this results? Thanks in advance, Miguel Angel

Anonymous posted a comment on discussion BayesAss Q&A

Agree. Any advance with this issue?

Anonymous posted a comment on discussion BayesAss Q&A

.exe not work on windows 10. That to make? Thanks.

Anonymous posted a comment on discussion BayesAss Q&A

Dear all. I am trying to estimate the gene flow by BayesAss with referring to the manual. We run the analysis under the following conditions. The acceptance rate of individual migrant ancestries was zero, and the output results did not seem to properly evaluate gene flow. What are the possible causes? ...... BA3Win64SNP.exe -v -g -t -s100 -i100000000 -b20000000 -n2000 -a0.6 -f0.3 -o 100000000.txt BayesAss_format.txt ...... Input file: BayesAss_format.txt Output file: 100000000.txt Individuals: 257...

Anonymous posted a comment on discussion BayesAss Q&A

Can SNP data from resequencing be used in Bayesass software? Or is migration-n more appropriate?

Anonymous posted a comment on discussion BayesAss Q&A

Dear Dr. Rannala I have problems with my input file, i would like if you can give me an example of it for microsatellites data

Anonymous posted a comment on discussion BayesAss Q&A

Hi Dr. Rannala, I am new to BA3 and am having issues trying to get my DeltaF accepted % to between 20 and 60. I have tried adjusting deltaF several times (to 0.3, 0.5, 0.8 and 1.0), but every time the accept % is 0.0. My other parameters deltaA and deltaM are fine, but I'm not sure why this is? Any help would be greatly appreciated! Many thanks, Rosie

Anonymous posted a comment on discussion BayesAss Q&A

This worked for me as well!!

Rannala posted a comment on discussion BayesAss Q&A

As explained in the documentation the standard deviation is presented in the output file in parentheses next to the estimate of posterior mean migration proportion. A 95% credibility interval is approximately as mean +/- 2*sdev.

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I've been playing with BayesAss on a dataset with 13 populations with quite low subdivision (average around 0.03 fst). After playing with mixing parameters and getting acceptance rates within the recommended thresholds, the trace still osciliates up and down more than I'd like after the initial increase, even with very long chains. I was wondering if this might be the result of there being too little subdivision between populations. Is there a known point at which BayesAss becomes pointless?...

Anonymous posted a comment on discussion BayesAss Q&A

Hi AM, Just curious about your second question "how can I calculate the 95% confidence intervals?" Have you solved that? Cheers, RJ

Anonymous posted a comment on discussion BayesAss Q&A

I'm trying to install BayesAss 3.0.4 - I've tried using the command prompt, using Cygwin and on a linux server but I keep getting various gsl errors. I've then tried installing gsl (even though it should already be part of Cygwin and I'm fairly certain it's already on my linux server too) but that presents more errors. The errors specify issues with: libgsl-0.dll gsl/gsl_sf_gamma.h I've spent hours trying to work this out... please, somebody help! :(

Anonymous posted a comment on discussion BayesAss Q&A

I want to use BayesAss for microsatellite data. Please any one can guide data format that can read by BayesASS? Arjun

Anonymous posted a comment on discussion BayesAss Q&A

Hello, I have the problem about un-decreased acceptance rates. I have 313 individuals and 11 SSR locus. All of the acceptance rates are quite high(above 0.9), but when I analysied the trace file in Tracer software, it was converged. Does it matter if about the acceptance rates in this situation? Suggestions and comments on this issue will be really appreciated! Best wishes, WEI Xu

Anonymous posted a comment on discussion BayesAss Q&A

I have windows 10. When attempt to execute the program "executable" ver 3, not to work. That to make? Thanks.

Anonymous posted a comment on discussion BayesAss Q&A

Hello, I just have a general question about the software. The majority of the genetic studies, like mine, used unlinked loci for the genetic analysis. I did a linkage desiquilibrium analysis (GenePop) to discard the gene with disequilibrium. After, I used BAYESASS to estimate the genetic flow. But I don't understand how BAYESASS detect the state of each individual (resident/immigrant) if the loci are in linkage equilibrium. Because, this software used the gametic disequilibrium due to migration....

Anonymous posted a comment on discussion BayesAss Q&A

Hi there I have just started using BayesAss software a few weeks ago. i have managed to get the input file in the right format however, it can only detect one population and further analysis is not conducted. Can you please kindly advice on what the problem might be, thanks.

Anonymous posted a comment on discussion BayesAss Q&A

Dear all. Good evening. I used BayesAss and had a trouble. I want to get 95 % confidence interval and the user manual also recommends us to get it. But I don't know how to get or calculate it. thank you. tkhr

Rannala posted a comment on discussion BayesAss Q&A

I have compiled BPP for use with large SNP or microsatellite datasets. The filres for Mac and Windows are available here.

Anonymous posted a comment on discussion BayesAss Q&A

Dear Dr. Rannala and BayesAss users. I am trying to estimate contemporary gene flow among fish populations in Caribbean reefs using SNP data. I have not been able to place the acceptance rates of the paramenters within 20-60%. I assume it is because there is not enough information in the data. To gain more info, I would like to run the full data 10,059 SNPs (so far I have tried with a 400 SNP subset). I wonder how could I modify the program to run it on the 10,059 SNP dataset. Of the runs that I...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, If you get this can you pleasepost a copy of modified program? I would like to apply it to a large SNP data set as well. Thanks, Matt

Anonymous posted a comment on discussion BayesAss Q&A

hi,is the problem solved?

Anonymous posted a comment on discussion BayesAss Q&A

Guys, does anyone know where I can find information about the program's history? Information of the type who created it, the year it was released, and all the reviews it makes?

Rannala posted a comment on discussion BayesAss Q&A

BayesAss should be suitable. I suggest that you try it.

Rannala posted a comment on discussion BayesAss Q&A

Please send me your input file brannala@ucdavis.edu and I can have a look. Bruce

Anonymous posted a comment on discussion BayesAss Q&A

Dear Bruce - would it be possible to implement in BayesAss (and possibly in BayesAssNM...

Anonymous posted a comment on discussion BayesAss Q&A

Hello, I wonder if BayesAss accept microsat data either as number of repeats or length...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I am very new to the BayesAss. I am greatly happy that I can play out your program...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, Actually I have also some issues running the software. My first run worked properly...

Anonymous posted a comment on discussion BayesAss Q&A

I’ve just installed BayesAss 3.0.4 for Windows 7 (32-bit). When I click on the executable...

Anonymous posted a comment on discussion BayesAss Q&A

Hi ye all! We would be very happy for any insigth into how to correctly compare estimates...

Anonymous posted a comment on discussion BayesAss Q&A

Hope this isn't a dead feed being over a year since that last message, but I am trying...

Anonymous posted a comment on discussion BayesAss Q&A

Dr. Rannala, I'm having a similar issue to the post made on 2016-01-20 by a different...

Anonymous posted a comment on discussion BayesAss Q&A

I'm wanting to test contemporary migration between fish populations in a river system....

BayesAss released /BA3/3.0.4/BA3NGS.zip

Mu-Yeong Lee posted a comment on discussion BayesAss Q&A

Dear All, I am very new to the BayesAss. I am greatly happy that I can play out your...

amandine marie` posted a comment on discussion BayesAss Q&A

I already did it but it doesn't work...

Anonymous posted a comment on discussion BayesAss Q&A

It sounds like you may have tried running it by duble clicking on the executable...

amandine marie` posted a comment on discussion BayesAss Q&A

Hello, I just download the version 3.04 to use it on my laptop windows 8, 64 bits....

Rannala posted a comment on discussion BayesAss Q&A

You can use gene sequences by coding each distinct sequence as a different allele....

Rannala posted a comment on discussion BayesAss Q&A

I would not recommend using mtDNA sequences. The current program is designed for...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I have a touble that does the BAYEASS can run with gene sequences? if can, what...

Anonymous posted a comment on discussion BayesAss Q&A

hello,I have met the same problem.What should I do ?

Anonymous posted a comment on discussion BayesAss Q&A

hello, I have the same problem. My data include 240 individuals,5 populations and...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I am having issues understanding my results after running BayesAss v3. The program...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I am coming accross the "Segmentation fault 11" error message when running BayesAss...

Anonymous posted a comment on discussion BayesAss Q&A

I have the same problem with installing 3.0.3. onto a 64 bit windows 7 computer....

Anonymous posted a comment on discussion BayesAss Q&A

I try to change the three parameters (a,f,m) in order to get the optimal acceptance...

Anonymous posted a comment on discussion BayesAss Q&A

Dear Dr. Rannala, I am investigating gene flow between two populations with very...

Anonymous posted a comment on discussion BayesAss Q&A

Hello, Is there a limit to the number of loci BayesAss 3 can process? The manual...

Anonymous posted a comment on discussion BayesAss Q&A

Hi, I am trying to analysis recent migration among three populations using multilocus...

Anonymous posted a comment on discussion BayesAss Q&A

Ok, that's clear then. Thanks! :) <ahem> not at all good with unix... ;) just fluently...

Rannala posted a comment on discussion BayesAss Q&A

I have posted a new version of the program with an option "-p" that runs the program...

Rannala posted a comment on discussion BayesAss Q&A

I have compiled a version of BA3 for Mac OS X version 6 and earlier. Using this version...

Anonymous posted a comment on discussion BayesAss Q&A

same problem! plus not working on PC....really not very user friendly this softw...

Rannala posted a comment on discussion BayesAss Q&A

I have posted a new version of BA3 that corrects two minor bugs in the priors on...

BayesAss released /BA3/3.0.4/src/BA3-3.0.4.tar.gz

BayesAss released /BA3/3.0.4/docs/BA3Manual.pdf

BayesAss released /BA3/3.0.4/BA3Windows32.zip

BayesAss released /BA3/3.0.4/BA3Windows64.zip

BayesAss released /BA3/3.0.4/BA3-Windows-64.zip

BayesAss released /BA3/3.0.4/BA3-3.0.4.OSX-pre7.zip

BayesAss released /BA3/3.0.4/BA3-3.0.4.OSX-post7.zip

BayesAss released /BA3/3.0.4/BA3-3.0.4.OSX-post7.tar.gz

Rannala posted a comment on discussion BayesAss Q&A

Okay, I understand what is going on. The command line options should follow standard...

Anonymous posted a comment on discussion BayesAss Q&A

Ok, I have done several test runs and it seems that the -s=xxxx gives me the Random...

Anonymous posted a comment on discussion BayesAss Q&A

Actually when I changed the -s=xxxx to -s10xxxx it works. :D So, no problems anymore....

Rannala posted a comment on discussion BayesAss Q&A

Can you send me your input file as well as the exact command line options that you...

Rannala posted a comment on discussion BayesAss Q&A

The results from 1.3 should be fine. I have compared 1.3 and 3.* output for consistency...

Anonymous posted a comment on discussion BayesAss Q&A

Hi there! Happily using the new command line version 3.0.3 under Windows (7). Previously...

Anonymous posted a comment on discussion BayesAss Q&A

I am interested in running BayesAssNM but I don't have a Linux-running computer....

Anonymous posted a comment on discussion BayesAss Q&A

my acceptance rate for migration rate is very low 0.03-0.07 I have modified the migration...

Anonymous posted a comment on discussion BayesAss Q&A

Is there any way to get the trace file to calculate the Bayesian deviance in the...

Anonymous posted a comment on discussion BayesAss Q&A

Dear Bruce, Because of installation problems I had to use the version BayesAss1.3....

Anonymous posted a comment on discussion BayesAss Q&A

Dear Dr. Rannala, I am using Bayesass to estimate posterior probabilities for individual...

Anonymous posted a comment on discussion BayesAss Q&A

I have just downloaded V3.0.3 to Windows 7 and Windows 8 and I am getting the error...

Rannala posted a comment on discussion BayesAss Q&A

This will happen when the data are not very informative and therefore the likelihood...

Rannala posted a comment on discussion BayesAss Q&A

The slight drop in logP is probably due to the fact that the chain is initiated with...

OS Klanten posted a comment on discussion BayesAss Q&A

Hi I have tried to compile BayesASS v. 3 on my MAC (Yosemite) 10.10.3 (processor...

melissa posted a comment on discussion BayesAss Q&A

I too (along with everyone else I presume) need to use these results. Are you really...

Rannala posted a comment on discussion BayesAss Q&A

It is normal for acceptance rates to increase as the chain runs. I suggest that you...

Rannala posted a comment on discussion BayesAss Q&A

There is no option for a trace plot in BayesAss 1.3. If you instead use BA 3 you...

Rannala posted a comment on discussion BayesAss Q&A

I have never tried running a dataset that size. If you send me the input file I can...

Rannala posted a comment on discussion BayesAss Q&A

I suspect that something is wrong with the input file. If you email me the input...

Rannala posted a comment on discussion BayesAss Q&A

I suspect that the files are being created somewhere on your machine. When you are...

Rannala posted a comment on discussion BayesAss Q&A

No, the program is not valid for use with haploid organisms. If the haploid organisms...

Rannala posted a comment on discussion BayesAss Q&A

Actually, in the manual example BA3 is executed in the local directory. If you use...

Rannala posted a comment on discussion General Discussion

Yes, you are correct. Generally, m_ii values greater less than about 70% indicate...

Rannala posted a comment on discussion BayesAss Q&A

When using discrete parameters in MCMC (in this case the individual migrant ancestries...

Rannala posted a comment on discussion BayesAss Q&A

This sounds like a file format problem. Perhaps the file conversion was not successful....

Wubetu posted a comment on discussion BayesAss Q&A

Can you please change this file to BA3 input file form.

Rannala posted a comment on discussion BayesAss Q&A

Can you send me your input file? I would like to look at the behavior of the chain...