Issues
- 6
Only output log file but can not genenrate the json file
#1757 opened by aaannaw - 10
Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found. Failed constraint:relax.ge.omega2
#1745 opened by fuesseler - 8
Error processing my job at DataMonkey
#1758 opened by Zafar-iq - 2
KH test on GARD results
#1746 opened by Oliveira-Hugo - 3
DataMonkey Error Message: "- had 7747 sites"
#1752 opened by hannahg3009 - 5
HyPhy MEME Positive Selection at 0 Branches?
#1740 opened by singing-scientist - 8
omega from internal branches
#1755 opened by evandiego83 - 5
MEME HyPhy killed by signal 15
#1736 opened by moonless00 - 5
GARD execution error
#1739 opened by liamxg - 3
Barely any parallelism (max 110% CPU) running `hyphy gard` on macOS arm64
#1730 opened by corneliusroemer - 8
GARD crashes when run on 27 SARS-CoV-2 sequences
#1731 opened by corneliusroemer - 13
Format for selecting branches to test on FEL
#1734 opened by andrearam28 - 3
The dN/dS ratio shows a significant difference between the foreground and background sets. Why is the result still that selection is not associated with the phenotype/trait?
#1737 opened by uyghbo - 6
Brew Cask install is extremely out of date
#1753 opened by ethanagon - 1
Problem with reading trees in Datamonkey
#1756 opened by lorsenex - 2
No HYPHYMPI option
#1751 opened by lorsenex - 1
Simulate sequences from branch specific omega values
#1754 opened by sophie-03 - 6
Usage of MNMs in BUSTED
#1749 opened by mridna - 7
Does excluding species with paralogous sequences violate aBSREL and/or RELAX assumptions of single-copy orthology?
#1725 opened by pkfsantos - 3
Interpretation of RELAX across many genes
#1726 opened by kferger320 - 4
suggestions about running negative selection analysis - if thats what happening
#1748 opened by sapuizait - 10
How to process the results files from OrthoFinder into input files for HyPhy ABSREL？
#1723 opened by SWei2333 - 3
How to choose background branches?
#1724 opened by Buckaroo1 - 12
Different aBSREL results for same inputs
#1722 opened by glitterseaworms - 6
FEL ANALYSIS doubts
#1747 opened by Naniogui - 5
MEME interpretation - 0 branches?
#1721 opened by glitterseaworms - 4
Error on MEME
#1741 opened by andrearam28 - 2
Inconsistent results from MEME
#1744 opened by katherinermartin - 4
GARD error on Datamonkey
#1742 opened by thersyl - 2
MEME EBFs vs # branches
#1743 opened by dcaffrey - 2
FADE: substitution model selection
#1727 opened by ewysocka - 2
- 11
- 7
- 3
Multi-ORF Analysis Questions
#1728 opened by singing-scientist - 2
test for detecting compartmentalization in dataMonkey
#1719 opened by BlasiMar - 2
DataMonkey not recognizing forground branches
#1720 opened by ebraun68 - 5
Analysis ends but does not progress to report generation
#1717 opened by hkunerth - 5
Persistent error when running Gard
#1713 opened by MiloEliot - 4
How to select positive signals of the foreground branch from the results of aBSREL modle
#1714 opened by aaannaw - 5
Multiple Testing Correction in BUSTED vs absREL
#1707 opened by NicMAlexandre - 9
BUSTED error: tree_id_0 is not a supported object type in call to SetParameter
#1710 opened by 00-kelvin - 2
- 2
- 5
aBSREL run time
#1712 opened by lagphase - 2
What is HyPhy calling the 2 nodes pointed at with arrows in this tree (image and txt file attached)?
#1711 opened by glitterseaworms - 3
Error: Internal error Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found. Set it by hand, or check your constraints for compatibility.
#1709 opened by glitterseaworms - 4
When does RELAX collapse rate classes?
#1708 opened by NatJWalker-Hale - 0
- 1
FEL not working - Error included
#1703 opened by SculpturatusLabs