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kfuku52
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csubst
Molecular convergence detection
BSD 3-Clause "New" or "Revised" License
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Species or gene tree?
#59
bmm514
opened
3 months ago
3
How to identify convergent sites by csubst?
#58
xinghua1001
opened
4 months ago
3
IndexError: list index out of range
#57
kfuku52
closed
6 months ago
1
Foreground branch combinations mixed for multiple traits with --fg_format 2
#56
kfuku52
closed
7 months ago
1
There is no target branch combination at K = 2.
#55
kfuku52
closed
7 months ago
2
--fg_clade_permutation is broken in v1.4.0
#54
kfuku52
opened
7 months ago
0
Including all branch combinations with --fg_clade_permutation
#53
kfuku52
opened
7 months ago
0
ValueError:Quantiles
#52
agneeshbarua
closed
8 months ago
5
Questions and general guidance
#51
francicco
opened
8 months ago
24
Loading foreground-only ancestral states with --exhaustive_until 1
#50
kfuku52
opened
9 months ago
0
Malformed selection error in csubst_site
#49
agneeshbarua
closed
9 months ago
3
How can I set the path of the output files?
#48
s1fa
closed
10 months ago
1
prioritize convergence in conserved sites
#47
kfuku52
opened
11 months ago
0
P value for excess convergence
#46
kfuku52
opened
11 months ago
0
How to find which gene is selected
#45
YecLab
closed
1 year ago
3
interpreting results of csubst
#44
yimingweng
closed
11 months ago
7
Questions for calculating convergent gene
#43
YecLab
closed
1 year ago
5
tree + site plot in csubst site
#42
kfuku52
opened
1 year ago
5
Number of independent branch combinations: 0
#41
kfuku52
closed
1 year ago
1
AttributeError: module 'numpy' has no attribute 'bool'.
#40
kfuku52
closed
1 year ago
0
AttributeError: 'NoneType' object has no attribute 'is_lineage_foreground'
#39
kfuku52
closed
1 year ago
1
Error during instantaneous rate matrix generation
#38
agneeshbarua
closed
1 year ago
5
csubst site --mode
#37
kfuku52
opened
1 year ago
2
Print substitutions in the b table
#36
kfuku52
closed
1 year ago
1
urllib.error.HTTPError: HTTP Error 404: Not Found
#35
kfuku52
closed
1 year ago
0
Interpreting w_C = Inf values
#34
aleungplants
closed
1 year ago
3
IndexError: list index out of range
#33
kfuku52
closed
1 year ago
0
AttributeError: 'NoneType' object has no attribute 'get_leaf_names'
#32
kfuku52
closed
1 year ago
1
ValueError: cannot mmap an empty file
#31
kfuku52
closed
1 year ago
1
UnboundLocalError: local variable 'cb' referenced before assignment
#30
kfuku52
closed
1 year ago
0
AttributeError: module 'numpy' has no attribute 'int'
#29
dupillir
closed
1 year ago
2
Supporting user-provided alignment in csubst site
#28
kfuku52
closed
1 year ago
0
pandas FutureWarning
#27
kfuku52
closed
1 year ago
0
ValueError: min() arg is an empty sequence
#26
kfuku52
closed
1 year ago
0
AttributeError: 'bool' object has no attribute 'sum'
#25
kfuku52
closed
1 year ago
1
FutureWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array.
#24
kfuku52
closed
1 year ago
0
new notation
#23
kfuku52
closed
2 years ago
0
reporting hydrophobicity change in csubst_site.tsv
#22
kfuku52
closed
2 years ago
1
Rows in custom transition matrix do not sum to 0.
#21
kfuku52
closed
2 years ago
0
branch_id order
#20
kfuku52
closed
1 year ago
0
RuntimeError in python 3.9 with multiple processes
#19
kfuku52
closed
2 years ago
1
MemoryError
#18
kfuku52
closed
3 years ago
3
spe2any in submodel output
#17
kfuku52
closed
2 years ago
1
deprecate --parallel_mode and change --threads to --ncpu
#16
kfuku52
closed
1 year ago
2
support uniprot info retrieval
#15
kfuku52
opened
3 years ago
1
support --foreground_mrca option
#14
kfuku52
closed
1 year ago
0
struct.error: 'i' format requires -2147483648 <= number <= 2147483647
#13
kfuku52
closed
2 years ago
1
Handling the cb table as a memory map
#12
kfuku52
opened
3 years ago
0
check csubst N_sub and S_sub to see if pyvolve's omega should be adjusted twice.
#11
kfuku52
closed
3 years ago
1
Incompatible --ml_anc no --calc_quantile yes
#10
kfuku52
closed
3 years ago
0
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