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matsengrp
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antigen
Simulating virus evolution and epidemiology
http://bedford.io/projects/antigen/
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sample host immune histories
#30
zorian15
closed
2 months ago
0
Group epitopes based on low or high mutation effect
#29
thienktran
opened
1 year ago
0
27-purifying-selection
#28
zorian15
closed
1 year ago
0
Add "purifying selection" to sequence simulation
#27
zorian15
closed
1 year ago
0
25 true fitness
#26
zorian15
opened
1 year ago
1
Add "true fitness" metric to tips file
#25
zorian15
opened
1 year ago
0
Random epitope mutations
#24
thienktran
closed
1 year ago
5
At the beginning of the simulation, make sure that viruses are initiated with the input sequence instead of a random sequence
#23
Haddox
opened
2 years ago
0
New GeometricSeqPhenotype class
#22
thienktran
closed
1 year ago
7
update mutation model to mimic an HKY85 model
#21
Haddox
opened
2 years ago
3
send Thien H3N2 nucleotide sequence used in Bloom-lab DMS
#20
Haddox
closed
2 years ago
0
Add functionality to run simulations in batches
#19
zorian15
closed
1 year ago
7
16-genealogical-pi
#18
zorian15
closed
2 years ago
1
Combining `GeometricPhenotype` with `SequencePhenotype`
#17
zorian15
closed
1 year ago
8
Calculating and reporting genealogical pie
#16
zorian15
closed
2 years ago
0
14 simulation names
#15
zorian15
closed
2 years ago
1
Enable naming of simulation outputs.
#14
zorian15
closed
2 years ago
0
Added different cross immunity functions to SequencePhenotype
#13
thienktran
closed
2 years ago
1
Modularize alphabet to have different valid characters
#12
thienktran
closed
2 years ago
0
Allow SequencePhenotype to use nucleotides or amino acids
#11
thienktran
closed
2 years ago
0
Added SequencePhenotype class
#10
thienktran
closed
2 years ago
0
Cluster out.tips using sklearn
#9
thienktran
closed
2 years ago
0
1 update mutate
#8
thienktran
closed
2 years ago
0
Kickstart unit testing w/ J-Unit.
#7
zorian15
closed
2 years ago
0
Cluster using scikit-learn
#6
thienktran
closed
2 years ago
0
SequencePhenotype Unit tests
#5
zorian15
closed
2 years ago
1
Resolving issue #1. Enable mutate() to substitute
#4
thienktran
closed
2 years ago
0
Implement a new function of Cross-Immunity
#3
thienktran
closed
2 years ago
2
Enable SequencePhenotype to work with PhenotypeFactory
#2
thienktran
closed
2 years ago
0
Update mutate() to perform substitutions
#1
thienktran
closed
2 years ago
0