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42 Open 17 Closed
42 Open 17 Closed
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Issues list

remove-duplicates.bf seems to also remove tree annotations
#67 opened Dec 19, 2024 by 00-kelvin
3
error with clean-names.bf
#66 opened Dec 19, 2024 by 00-kelvin
7
choose test branches for relax selection
#63 opened Nov 27, 2024 by xing-he529
two runs for the same hyphy relax command, but the results are different
#62 opened Nov 26, 2024 by aaannaw
"Not supported by data" and " Collapsed rate class " in the log file
#61 opened Nov 26, 2024 by aaannaw
Question Regarding Relax Analysis Results (K = 0)
#60 opened Nov 22, 2024 by aaannaw
2
Unexpectedly High Proportion Genes Showing Relaxed Selection in HyPhy RELAX Analysis
#59 opened Nov 20, 2024 by jdaron
3
Only output log file but can not genenrate the json file
#58 opened Nov 10, 2024 by aaannaw
Calculate global kappa
#56 opened Sep 16, 2024 by sophie-03
3
MCMCtree
#55 opened Aug 22, 2024 by ofedrigo
how to label background as green?
#54 opened Aug 18, 2024 by liamxg
Contrast-FEL analyses
#53 opened Jul 13, 2024 by JJohnSmith
2
BUSTED-PH results not symmetric when exchanging foreground and background labels
#51 opened Apr 5, 2024 by tlinksvayer
2
--remove-duplicates
#50 opened Mar 21, 2024 by sjellerstrand
1
If the branch lenghth in species tree are necessary in my analysis using hyphy?
#49 opened Feb 23, 2024 by Neo-xbx-00
label-tree.bf is rerooting trees when I do not want it to
#48 opened Dec 12, 2023 by liamfriar
3
Calculating gene wide dn/dS on foreground vs. background branches
#47 opened Nov 20, 2023 by yashsondhi
2
RELAX-scan crashes with latest hyphy
#42 opened Jun 29, 2023 by dgkontopoulos
1
how to FitMG94 reports trees scaled on dS, dN and dN/dS
#41 opened Jun 21, 2023 by sushidaren
1
Labeling phylogenetic tree programatically
#40 opened Jun 19, 2023 by KittyMurphy
9
BUSTED-PH with large number of sequences
#39 opened Jun 9, 2023 by rsiani
3
BUSTED-MH are running two slowly
#38 opened Jun 7, 2023 by jinglkang
@spond
6
Question pre-msa.bf sequence order
#36 opened Feb 28, 2023 by kullrich
2
Question on appropriate use of BUSTED-PH
#35 opened Feb 17, 2023 by Emilyaoc
1
Issue with pre-msa.bf
#34 opened Feb 14, 2023 by lakshsesh97
5
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