Activity for codonPhyML
-
Fernanda Giersdorf posted a comment on discussion Users
sorry, I mixed up the options from phyml with codonphyml and cant delete the topic.
-
Dear developers, when running codonphyml -i alignment_noStop.phy -d codon -b 100 -w --fmodel F3X4 i get an error . Launch bootstrap analysis on the most likely tree... Segmentation fault (core dumped) this only happens when using the bootstrap option, regardless of the number of bootstraps. without the bootstrap option, the program runs without any issues. Attached is the alignment file used. Do you have suggestions on how to fix this? Thank you! Fernanda
-
Marcelo S Zanetti posted a comment on discussion Users
Hello Minh, Thank you for your message and sorry for the late reply. You have to set an environment variable. Check this link: http://software.intel.com/en-us/mkl-windows-developer-guide-setting-the-number-of-threads-using-an-openmp-environment-variable I am planning to be more active this year. Should you require further assistance, let me know! Best
-
Anonymous posted a comment on discussion Users
Dear developers, I saw that codonPhyML has a omp version to utilize multicore, which is very nice compared with PhyML to reduce waiting time. I could compile the program already. However, I could not find anywhere how to specify the number of cores/threads to use. Can you please help? Thanks, Minh
-
Hi Andrey. Thank you for your feedback. I will redirect the error messages to a log...
-
Andrey Rozenberg modified a comment on discussion Users
The --quiet option doesn't prevent the program from prompting for user input in case...
-
The --quiet option doesn't prevent the script from prompting for user input in case...
-
The --quiet option doesn't prevent the script from prompting for user input in case...
-
Hi Sorry for the late reply again! So you try to run the exact command line above...
-
Hi Sorry for the late reply again! So you try to run the exact command line above...
-
Anonymous posted a comment on discussion Users
Hi, I'm getting the same error. Was there a solution? Cheers
-
Hi sorry for the late reply. Last semester was a busy one. Can you please attach...
-
Anonymous posted a comment on discussion Users
Hi, when I try to run codonphyml with the following command line (the input file...
-
Anonymous posted a comment on discussion Users
Hi, I have alignment in which some sequences are complete and start from first nucletide...
-
Hi Marcin, sorry for the late reply. Moved to another place last semester, and did...
-
Great!
-
codonPhyML released /codonphyml_multi.tgz
-
Peter Thorpe posted a comment on discussion Users
Great, thanks! I will use the trees generated. Thanks, Pete
-
Hi Peter, cool. I deleted some messages so it reads better now. While I am not read...
-
Hi Marcelo, Sorry your reply get nested in the conversation above (i didnt see it)...
-
Hi Peter, are you satisfied with my answer? Please let me know. Thx.
-
sorry for the late reply, wrote above.
-
Hi Peter, sourceforge was offline so I could not reply before. So you are using the...
-
Hi Peter, sourceforge was offline so I could not reply before. So you are using the...
-
Hi Peter, sourceforge was offline so I could not reply before. So you are using the...
-
Hi Peter, I am sorry, too many things to do, ended up forgeting your question. Will...
-
Thank you for the explanations above. Can I ask you about the 4 DN/DS values again?...
-
Thank you for the explanations above. Can I ask you about the 4 DN/DS values again?...
-
Cool, thank you for the explanation. Sounds very interesting. I will take a look...
-
HI Marcelo, Thank you very much for taking the time to discuss this will me!!!! Much...
-
Hi Peter, Thank you for using Codonphyml. I see you are confused with some concepts....
-
Hi Peter, Thank you for using Codonphyml. I see you are confused with some concepts....
-
Hi Peter, Thank you for using Codonphyml. I see you are confused with some concepts....
-
Hi Peter, Thank you for using Codonphyml. I see you are confused with some concepts....
-
Hi Peter, Thank you for using Codonphyml. I see you are confused with some concepts....
-
Hi Peter, Thank you for using Codonphyml. I see you are confused with some concepts....
-
Dear Users - please help!!, I have run CodonPhyml on my DNA/aligned orthologous clusters...
-
Ok, don't hesitate to write if you have any further problems. Best!
-
Stefan committed [r309]
added changelog and version number
-
Added AB aa model by Alexander Mirsky
-
Hi Ramiro, this is the answer I got from Dr. Anisimova, she developed the aLRT method....
-
Hi Ramiro, this is the answer I got from Dr. Anisimova, she developed the aLRT method....
-
Hi Ramiro, sorry for the late reply. Sourceforge is not notifying me correctly on...
-
Hi Ramiro, sorry for the late reply. Sourceforge is not notifying me correctly on...
-
Hi Greta, Thank you again! The model selection is still in the TODO list :-), sorry...
-
Hi Greta, Thank you for your interest. The MAC binary does not support OpenMp neither...
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
inconsistency in parameter and manual description
-
Fixed bugs number 4 and numer 6 (sourceforge re...
-
John Denton also wrote this: "Would it be possible to get a version of the Windows...
-
Best between NNI and SPR is still broken
-
Commented out two sanity checks in file utilities.c, within function "Best_Of_NNI_And_SPR"....
-
Changed "int info;" to "int info=0;" in file models.c, function "PadeApprox". Must...
-
Compiling error in models.c PADEAPPROX
-
Changed "int info;" to "int info=0;" Must be caused by an extremely strict compiler...
-
Hi Cymon, sorry for the delay. I will look into it and will let you know asap. Thank...
1
