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Questions tagged [simulated-data]

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How to identify all descendents of a branch on a phylogeny

I'm trying to simulate the evolution of binary traits on phylogenies in R to end up with a dataset of the traits held by each tip. Starting at the root, at every timestep, new traits are added with a ...
Daniel Pelletier's user avatar
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Simulation software recommendation to confirm pipeline validity

I'm trying to detect convergent evolution in different samples of the same species. I'm just trying to see if past 20 generations the nucleotide frequency of snps under pressure converges somewhat for ...
gl00ten's user avatar
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Generate simulated bam for certain snps

I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
Shafayet Rahat's user avatar
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Protein-Protein Simulation using Gromacs

Can we do protein-protein simulation through Gromacs? if yes, can anyone teach me the correct procedure to get this done. Thank you,
Mahendra Singh's user avatar
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Can I use Aho-Corasick for epidemic spread simulation?

I found that with this string-finding algorithm, this algo can determine if a string(person) holds something(if he has sick, already got vaccinated, and et cetera.). I am trying to simulate an ...
Dan-Ryuki's user avatar