GADMA
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ctlab
Genetic Algorithm for Demographic Model Analysis
moments was updated and now some tests fail. For example, fsc file is read and mask is now different. Should check that and update tests.
Hey, My parameter file is: Output directory: GADMA/Output_sort_all_seq Input data: input.vcf, pop_order_new.txt Outgroup: False Sequence length:{HiC_scaffold_1: 100107381, HiC_scaffold_2: 105422710, HiC_scaffold_3: 84653302, HiC_scaffold_4: 71730761, HiC_scaffold_5: 82087087, HiC_scaffold_6: 72648741, HiC_scaffold_7: 206147042, HiC_scaffold_8:...
For momentsLD sequence length should be set as dictionary with length for each chromosome. There is not enough documentation about it (Issue #56). We need to add it.
Keyerror
Hello, I'm trying to run GADMA with dadi engine on a sf file of 2 pops and GADMA pops this error that I don't understand : ``` gadma -p param_file_Toronto_downsampled...
Hey, I am new to GADMA. I have installed GADMA2 and trying to run it on vcf file but I get the error pasted bellow. Could you please help. My...
GADMA reads custom models for different engines. For example, one could take model specified for dadi and ask GADMA to find its parameters. GADMA has its own interface for model...
There are a plenty of papers that should be cited when one is using GADMA. They can be found in the documentation but it will be more useful to put...
Hello, I've been trying to run GADMA2 to infer the demographic history of two closely related species. I was looking for a way of setting a lower bound for the...
Hi, Ekaterina - Thanks again for this incredibly useful program! I had a great experience using for 2-population models. Ultimately, I want to implement for a 3-population model, but GADMA...
Sometimes `gadma.optimize_ga` is using the following way: ``` popt = gadma.Inference.optimize_ga( data, func_ex, engine='dadi', args=pts, p_ids = p_ids, X_init= [p0], lower_bound=lower_bound, upper_bound=upper_bound, verbose=1) ``` In that case there is an...