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bomeara
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selac
Model by O'Meara, Chai, and Gilchrist for SELection on Amino acids and/or Codons
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R Phangorn - Error message: Error in data[, tree$tip.label] : subscript out of bounds
#33
sydelstan
closed
3 years ago
0
added max.aX arguments for selon fitting
#32
mikegilchrist
opened
5 years ago
0
added optional parameters max.a0, max.a1.factor, max.a2 for selon
#31
mikegilchrist
closed
5 years ago
1
removed unused function CreateAAFitnessMatrix() to avoid confusion.
#30
mikegilchrist
opened
5 years ago
0
Upstream/master
#29
mikegilchrist
opened
6 years ago
0
Expm Optimization
#28
GrahamDB
closed
5 years ago
1
Change defaults to have more starts and fewer optimization loops per start
#27
bomeara
opened
6 years ago
0
Error message if tree tip labels don't match the sequence labels
#26
AJBerle
opened
6 years ago
1
Allow for Polytomies
#25
AJBerle
opened
6 years ago
0
Detect stop codons and deal with them
#24
bomeara
opened
6 years ago
0
Error with incomplete codons
#23
dominicev
opened
6 years ago
0
added convergence window
#22
clandere
opened
6 years ago
0
force all log(bls) to real numbrs
#21
dominicev
closed
6 years ago
0
modifiable max iterations
#20
dominicev
closed
6 years ago
0
nsites fixe
#19
clandere
closed
6 years ago
1
selacHMM fixes
#18
clandere
closed
6 years ago
0
expose optimization fn as an option
#17
bomeara
closed
7 years ago
1
Precision for lik.diff
#16
bomeara
opened
7 years ago
0
Move all documentation to roxygen2
#15
bomeara
closed
6 years ago
0
RK now works with TreeTraversalODE
#14
mikegilchrist
closed
7 years ago
0
Runge-Kutta (ode45) working properly
#13
mikegilchrist
closed
7 years ago
1
added additional arguments to PlotPerAAFitness
#12
mikegilchrist
closed
7 years ago
0
Look at run time, think about optimization in C++
#11
bomeara
closed
7 years ago
0
How to do support region
#10
bomeara
opened
8 years ago
1
Possible: optimize physiochemical properties per site rather than discrete aa
#9
bomeara
opened
8 years ago
0
Fixed brlen optim tests, fixed aa optim tests
#8
bomeara
opened
8 years ago
0
Add checkpointing
#7
bomeara
opened
8 years ago
0
Compare to Yang & Nielsen through sims
#6
bomeara
closed
7 years ago
1
Rokas dataset
#5
bomeara
closed
7 years ago
0
Plant dataset
#4
bomeara
closed
7 years ago
0
Metazoa sample dataset
#3
bomeara
closed
7 years ago
0
Debug optimization
#2
bomeara
closed
7 years ago
0
Create testing example
#1
bomeara
closed
8 years ago
0