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dekoning-lab
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slim-tree
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Updated for new version of python and numpy so can be used with new c…
#105
ebrintn
closed
1 week ago
1
Bug with Conda
#104
ebrintn
closed
1 week ago
2
Allow users to change fitness profile
#103
ebrintn
opened
3 weeks ago
2
Examples
#102
ebrintn
opened
3 weeks ago
0
Redev is ready to go and be merged with main! All bugs have been thoroughly tested
#101
ebrintn
closed
1 month ago
0
Overwrite fasta files rather than append
#100
ebrintn
closed
1 month ago
1
Check tree to ensure branches are in generations
#99
ebrintn
closed
2 months ago
1
Fixed a couple of bugs in cladeReader.py
#98
ebrintn
closed
3 months ago
0
Unittests
#97
ebrintn
closed
3 months ago
0
what is a_file.txt ?
#96
afarineshp
closed
3 months ago
1
Unittests
#95
ebrintn
closed
3 months ago
0
Versioning issue
#94
ebrintn
closed
3 months ago
1
Option for neutral simulations without stop codons
#93
ebrintn
opened
3 months ago
0
stationary distributions -> option for users that have only one distribution
#92
afarineshp
closed
8 months ago
0
Missing documentation and examples throughout
#91
jasondk
closed
6 days ago
2
R script crashes when codon_stationary_distribution has only one column
#90
jasondk
closed
3 months ago
3
Weird bug in selection denominators
#89
ebrintn
closed
1 month ago
2
Afi
#88
ebrintn
closed
1 year ago
1
Afi
#87
ebrintn
closed
1 year ago
0
Dn/Ds analyses
#86
ebrintn
opened
1 year ago
3
Taxa names need separation by `_' not by space
#85
ebrintn
closed
3 months ago
1
Bug in taxa names in tree_nuc.fasta output file
#84
afarineshp
closed
3 months ago
1
For HPC make finding fitness into job
#83
ebrintn
closed
8 months ago
3
Print useful error when stationary distributions don't have titles
#82
ebrintn
closed
1 year ago
1
Automate input tree to generations
#81
ebrintn
opened
1 year ago
2
Sort output and put into folders
#80
ebrintn
opened
1 year ago
2
Merge redev with main
#79
ebrintn
opened
1 year ago
4
Bug in nonWF model
#78
ebrintn
closed
3 months ago
4
No output in consensus sequence sampling
#77
ebrintn
closed
1 year ago
1
Implement fitness calculations from codon stationary dists
#76
ebrintn
closed
1 year ago
1
Should we increase the default length of the burn-in?
#75
ebrintn
closed
6 days ago
3
Bug in haploidy
#74
ebrintn
closed
1 year ago
1
Users can't have a gene count>1 and a coding ratio of 1
#73
ebrintn
closed
1 year ago
1
WE NEED UNIT TESTS!!!
#72
ebrintn
closed
1 month ago
2
Bugs in protein contact maps
#71
ebrintn
closed
1 year ago
2
For protein based fitness effects - give option to not build contact map if map already exists
#70
ebrintn
closed
1 year ago
1
Update to yaml formatting for population file
#69
ebrintn
closed
1 year ago
1
Update to slim 4
#68
ebrintn
closed
1 year ago
2
Make slim-tree more user friendly
#67
ebrintn
closed
1 year ago
3
SLiM-Tree Paper
#66
ebrintn
opened
1 year ago
3
Numpy update - deprecated names
#65
johnpatramanis
closed
1 year ago
1
Calculate dN and dS by counting fixations
#64
ebrintn
closed
6 days ago
9
Project using Slim-tree
#63
johnpatramanis
closed
1 year ago
0
I realized that the reason those docs were deleted was because I had not merged should solve overwritten examples in issue #61
#62
ebrintn
closed
3 years ago
0
Requirements for publication
#61
ebrintn
closed
3 months ago
3
Erin
#60
ebrintn
closed
3 years ago
0
Added some more examples
#59
ebrintn
closed
3 years ago
0
Added files for examples
#58
ebrintn
closed
3 years ago
0
Added folders for example simulations and added ex1
#57
ebrintn
closed
3 years ago
0
Added script to calculate fitness from frequency
#56
ebrintn
closed
3 years ago
0
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