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hyphy-analyses
HyPhy standalone analyses
MIT License
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two runs for the same hyphy relax command, but the results are different
#62
aaannaw
opened
5 hours ago
0
"Not supported by data" and " Collapsed rate class " in the log file
#61
aaannaw
opened
6 hours ago
0
Question Regarding Relax Analysis Results (K = 0)
#60
aaannaw
opened
3 days ago
2
Unexpectedly High Proportion Genes Showing Relaxed Selection in HyPhy RELAX Analysis
#59
jdaron
opened
5 days ago
3
Only output log file but can not genenrate the json file
#58
aaannaw
opened
2 weeks ago
0
Trouble understanding assumptions of various tests
#57
Tapejara100
closed
3 weeks ago
0
Calculate global kappa
#56
sophie-03
opened
2 months ago
3
MCMCtree
#55
ofedrigo
opened
3 months ago
0
how to label background as green?
#54
liamxg
opened
3 months ago
0
Contrast-FEL analyses
#53
JJohnSmith
opened
4 months ago
2
Branch specific dN/dS values
#52
sophie-03
closed
4 months ago
5
BUSTED-PH results not symmetric when exchanging foreground and background labels
#51
tlinksvayer
opened
7 months ago
2
--remove-duplicates
#50
sjellerstrand
opened
8 months ago
1
If the branch lenghth in species tree are necessary in my analysis using hyphy?
#49
Neo-xbx-00
opened
9 months ago
0
label-tree.bf is rerooting trees when I do not want it to
#48
liamfriar
opened
11 months ago
3
Calculating gene wide dn/dS on foreground vs. background branches
#47
yashsondhi
opened
1 year ago
2
Label tree not writing the labels
#46
rsiani
closed
1 year ago
5
Output are not writing on the results.json file - BUSTED
#45
swantan
closed
1 year ago
3
control over removed sequences in remove-duplicates.bf
#44
Suirotras
closed
1 year ago
2
Could not read command file from 'libv3/all-terms.bf'
#43
Joeytbl
closed
1 year ago
4
RELAX-scan crashes with latest hyphy
#42
dgkontopoulos
opened
1 year ago
1
how to FitMG94 reports trees scaled on dS, dN and dN/dS
#41
sushidaren
opened
1 year ago
1
Labeling phylogenetic tree programatically
#40
KittyMurphy
opened
1 year ago
9
BUSTED-PH with large number of sequences
#39
rsiani
opened
1 year ago
3
BUSTED-MH are running two slowly
#38
jinglkang
opened
1 year ago
6
What tree to use for FitMG94?
#37
liamfriar
closed
1 year ago
4
Question pre-msa.bf sequence order
#36
kullrich
opened
1 year ago
2
Question on appropriate use of BUSTED-PH
#35
Emilyaoc
opened
1 year ago
1
Issue with pre-msa.bf
#34
lakshsesh97
opened
1 year ago
5
Using BUSTED-PH genome-wide with unequal sampling of test and background species
#33
mbarkdull
opened
1 year ago
1
fail to make
#32
Xiaojun928
opened
1 year ago
11
The problem of parsing RELAX results
#31
1221li
opened
1 year ago
1
Find outliers json output
#30
stevenweaver
closed
1 year ago
0
Installation error
#29
J-Calvelo
closed
1 year ago
2
RELAX-scan/RELAX.bf results
#28
francicco
opened
1 year ago
2
Failed to Resize Memory
#27
NicMAlexandre
opened
1 year ago
2
How to run pre-msa.bf
#26
NicMAlexandre
opened
1 year ago
2
Help with getting contrast-fel.bf to work on command line
#25
Emilyaoc
opened
2 years ago
6
Loading reference sequence
#24
abulenciamiguel
closed
2 years ago
0
Trouble running codon-msg
#23
marcelauliano
closed
2 years ago
1
SCUEAL-WG tool
#22
juanledesma78
opened
2 years ago
0
label-tree.bf - label more than one set
#21
IsaS89
closed
2 years ago
1
Input sequences aligments
#20
ritafonso
opened
3 years ago
2
Interpreting meaning of test results background p-value from BUSTED-PH
#19
mbarkdull
opened
3 years ago
0
Raw counts in MG94 output
#18
ekopania
opened
3 years ago
4
Output of FitMG94
#17
mlosilla
opened
3 years ago
2
install and run RELAX-scan
#16
mlosilla
opened
3 years ago
5
Filter output
#15
stevenweaver
closed
3 years ago
0
How to choose a foreground branch to test?
#14
astridlee
opened
3 years ago
4
dN, dS values
#13
kavithamallayaa
opened
4 years ago
17
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