# Tagged Questions

Models that analyse biological systems or processes using the tools of applied mathematics.

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### How many traits can a multivariate breeders equation handle?

The multivariate breeders equation (MBE) by Lande predicts the change in a trait $\Delta \bar z$ (response) as $\Delta \bar z = G \beta$ where $G$ is a genetic variance-covariance matrix and ...
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### Expected time for a neutral allele to reach a frequency of $p_1$ when starting at frequency $p_0$

Kimura and Ohta (1968) showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is $$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$ where ...
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### Basic Modelling in Quantitative Genetics

I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a ...
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### Queller's 1985 version of hamilton's rule

Queller 1985 ("Kinship, reciprocity and synergism in the evolution of social behavior") provides a generalization of Hamilton's rule that allows for non-additivity. To accomplish that, Queller writes ...
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### Eye color genetics

I am trying to find a model to link the phenotype eye color to its genotypes. I know that there exists a simple model from Davenport, which explains {brown,blue} eyes. Further, there is an extended ...
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### Experimental techniques to measure protein-protein and protein-ligand structure and dynamics

We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking ...
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### Is there a standard formula/calculation for sexual dimorphism?

Is there a standard, or most accepted, way to present a value for sexual dimorphism? For example, one could use $$\frac{\text{Female value}}{\text{Male value}} -1$$ This would give negative values ...
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### Mutation-Selection-Drift Equilibrium

mutation-selection-drift equilibrium is one of the most important concept of population genetics. I could easily find the calculations for mutation-secltion equilibrium and for mutation-drift ...
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### Mutation-drift equilibrium and among loci variance in heterozygosity

At mutation-drift balance, the increased heterozygosity brought by new mutations is exactly equal to the loss of heterozygosity due to genetic drift. At equilibrium, the expected heterozygosity for a ...
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### What is the probability of fixation for a mutant under fluctuating selection?

Here is an answer which explain how one can model the frequency of an allele that is under fluctuating selection (selection that varies through time). Not, thinking about fluctuating selection, there ...
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### Based on which criteria should i choose the control sample to calculate delta_delta_Ct

I want to calculate the gene expression of an experiment with the Delta delta Ct method. I have these results from two runs of a real time PCR (one for the GOI(Gene of Interest) and one for the ...
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### Effects of Genetic Drift on Linkage Disequilibrium

From what I understood of @Canadianer's answer here... Genetic drift randomly causes negative or positive linkage disequilibria, by changing allele frequencies through random sampling. Natural ...
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### Reverse complement of reconstruction model for assembling reads

One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this ...
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### Analytical Methods for Estimating Probability of Fixation

The probability of fixation $P$ of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to ...
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### Best software for protein in electric field modeling?

I'm trying to find a free, or cheap, software program to model the movement of a heterotrimeric protein in an alternating electric field. The dipole and crystal structure of the trimer are known. ...
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### General time reversible model of evolution and Felsenstein model

I would like to get suggestions for the books related to General time reversible model of evolution and Felsenstein model etc. Specifically the mathematical treatment of these topics and concepts ...