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PoonLab
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HexSE
Simulation of molecular evolution with overlapping reading frames
GNU General Public License v3.0
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Running HexSE eats a lot of RAM
#141
WilliamZekaiWang
opened
3 weeks ago
0
Make sequence input optional?
#140
ArtPoon
opened
3 weeks ago
1
Merge to incorporate getting overlap info and tests by Sandeep
#139
horaciobam
closed
1 year ago
0
Adding two new functions and corresponding tests
#138
SandeepThokala
closed
1 year ago
2
coverage report
#137
SandeepThokala
opened
1 year ago
4
Dev
#136
ArtPoon
closed
1 year ago
2
Added few fixes
#135
SandeepThokala
closed
1 year ago
0
Unit test: resolve ambiguities
#134
ArtPoon
closed
1 year ago
2
Document behaviour of scale and shape
#133
horaciobam
closed
1 year ago
3
Issue while testing `get_right_nt` method of Sequence class
#132
SandeepThokala
closed
1 year ago
1
Fixed all tests that broke.
#131
SandeepThokala
closed
1 year ago
3
Issues faced after running all test classes in tests\test_sequence_info.py
#130
SandeepThokala
closed
1 year ago
2
Test failures in TestReadORFs (.\tests\test_run_simulation.py)
#129
SandeepThokala
closed
1 year ago
0
Test failures in TestValidORFs (.\tests\test_run_simulation.py)
#128
SandeepThokala
closed
1 year ago
0
Import errors when running run_simulation.py
#127
SandeepThokala
closed
1 year ago
1
Allow user to specify how selective effects combine in overlapping regions
#126
ArtPoon
opened
1 year ago
1
variation in dS
#125
ArtPoon
closed
1 year ago
2
Omegas acting at the nucleotide level, not the codon level
#124
horaciobam
closed
1 year ago
2
enforced PEP8 style, adjusted weighting
#123
ArtPoon
closed
2 years ago
0
Overlapping regions accumulating more mutations than single ORF region
#122
horaciobam
closed
2 years ago
8
update unnitest with new changes
#121
horaciobam
closed
1 year ago
5
Lots of STOP codons detected due to ORF being on the complementary strand
#120
horaciobam
closed
2 years ago
1
test dN/dS distribution
#119
ArtPoon
closed
1 year ago
33
update the paper
#118
ArtPoon
closed
2 years ago
0
Handling inputs
#117
ArtPoon
closed
2 years ago
0
Invalid orfs causing indexing errors.
#116
horaciobam
closed
2 years ago
1
handling_inputs: unable to run YAML
#115
ArtPoon
closed
2 years ago
2
New layer and new encoding system for keying the branches on the event tree
#114
horaciobam
closed
2 years ago
14
Merging event tree and probability tree
#113
GopiGugan
closed
2 years ago
0
Merge Event Tree and Probability Tree
#112
horaciobam
closed
2 years ago
3
master branch is failing one unit test
#111
ArtPoon
closed
2 years ago
1
prob_tree update with a list of a tuple instead of a dict
#110
ArtPoon
closed
2 years ago
1
Even under high mutation rates (0.5) sites are beeing conserved
#109
horaciobam
closed
2 years ago
24
Change location for simulation log file
#108
horaciobam
closed
2 years ago
1
Error when trying to use very high mutation rates
#107
horaciobam
closed
2 years ago
3
Different distributions for different orfs when input is genbank file
#106
horaciobam
closed
2 years ago
1
Write instructions for running HBV example
#105
ArtPoon
closed
2 years ago
2
Installation using setup.py
#104
ArtPoon
closed
1 year ago
0
Write documentation for YAML input files
#103
ArtPoon
closed
2 years ago
1
Refactore event tree
#102
kwade4
closed
3 years ago
0
Issue100
#101
kwade4
closed
3 years ago
0
Allow user to set different gamma distributions for different ORFs
#100
ArtPoon
closed
3 years ago
3
Create LICENSE
#99
ArtPoon
closed
3 years ago
0
Latin hypercube sampling
#98
horaciobam
closed
1 year ago
1
Holmes article
#97
ArtPoon
closed
4 years ago
0
Run HyPhy over simulation outputs
#96
horaciobam
closed
3 years ago
13
Another way to calculate the denominator for the "omega probability"
#95
kwade4
closed
3 years ago
1
Record synonymous and non-synonymous mutations in tuple
#94
kwade4
closed
4 years ago
0
Additional omega branches in event tree and probability tree
#93
kwade4
closed
4 years ago
4
Selecting the same categories in every mutation
#92
horaciobam
closed
4 years ago
6
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