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dekoning-lab
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slim-tree
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Fixed bug in HPC version
#50
ebrintn
closed
3 years ago
0
Fixed bug in SLim-Tree-HPC
#49
ebrintn
closed
3 years ago
0
Erin
#48
ebrintn
closed
3 years ago
0
Removed unnecessary print statement
#47
ebrintn
closed
3 years ago
0
Finished fixing user provided ancestral sequence
#46
ebrintn
closed
3 years ago
0
Fixed problem with start/stop codons and updated way program allows f…
#45
ebrintn
closed
3 years ago
0
Fixed problem in SLiM-Tree-HPC
#44
ebrintn
closed
3 years ago
0
Fixed readme
#43
ebrintn
closed
3 years ago
0
Fixed bug
#42
ebrintn
closed
3 years ago
0
Fixed problem in SLiM-Tree-HPC
#41
ebrintn
closed
3 years ago
0
Updated frequency and fitness profiles with default population size a…
#40
ebrintn
closed
3 years ago
0
Fixed slim-tree so that ancestral protein was formed
#39
ebrintn
closed
3 years ago
0
Erin
#38
ebrintn
closed
3 years ago
0
Add computation of expected dN/dS
#37
ebrintn
closed
1 year ago
1
Make examples of simulations
#36
ebrintn
closed
2 years ago
0
Think about dominance in chromosome
#35
ebrintn
closed
1 month ago
0
Change mutation models
#34
ebrintn
closed
3 years ago
1
Erin
#33
ebrintn
closed
3 years ago
0
Uneven Population Splitting in non-WF models
#32
g-heemeryck
closed
3 years ago
2
Remove any named calls
#31
ebrintn
closed
3 years ago
0
Made min division the actual min instead of always 0.1
#30
ebrintn
closed
3 years ago
0
Notify user when mutation rate has reached threshold for lethality
#29
ebrintn
closed
3 years ago
0
Erin
#28
ebrintn
closed
3 years ago
0
Examine equations for protein structures
#27
ebrintn
closed
3 years ago
1
Allow user to specify fitness profiles
#26
ebrintn
closed
3 years ago
2
optimization with C
#25
ebrintn
closed
3 years ago
0
Fix start and stop codons
#24
ebrintn
closed
3 years ago
0
Merge pull request #22 from dekoning-lab/main
#23
ebrintn
closed
3 years ago
0
merged from main
#22
ebrintn
closed
3 years ago
0
Erin
#21
ebrintn
closed
3 years ago
0
Optimized fitness function
#20
ebrintn
closed
3 years ago
0
Added __main__ file
#19
ebrintn
closed
3 years ago
0
Optimize fixation counting
#18
ebrintn
closed
3 years ago
1
Optimize fitness functions
#17
ebrintn
closed
3 years ago
2
Erin
#16
ebrintn
closed
3 years ago
0
Add unit tests to make sure everything works as required
#15
ebrintn
closed
3 years ago
1
Updated how SLiM-Tree runs fitness functions so that known genomes ca…
#14
ebrintn
closed
3 years ago
0
Allow users to model haploid organisms
#13
ebrintn
closed
3 years ago
1
Fixed bug in genomes with a single gene and added capability to outpu…
#12
ebrintn
closed
3 years ago
0
Updated Readme
#11
ebrintn
closed
3 years ago
0
Visualize contacts in protein based fitness effects
#10
ebrintn
closed
3 years ago
1
Write __main__ file to simplify usage
#9
ebrintn
closed
3 years ago
0
Fix read me file to include new options
#8
ebrintn
closed
3 years ago
0
Give option to output consensus sequence rather than just genomes of all or a subset of the individuals
#7
ebrintn
closed
3 years ago
0
Create SLiM-Tree manual/documentation
#6
ebrintn
closed
3 years ago
2
Add fitness effects based on protein structure
#5
ebrintn
closed
3 years ago
4
Appropriately model stop and start codons
#4
ebrintn
closed
3 years ago
3
Add option to model fitness shift and drift over time
#3
ebrintn
closed
3 years ago
2
Allow user to specify their own ancestral genome and heterogeneous profiles based on profile instead of randomly selecting
#2
ebrintn
closed
3 years ago
4
Distinguish between substitutions and polymorphisms
#1
ebrintn
closed
3 years ago
3
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