Blog-like notes

LaTeX for fly genetics

In fly genetics, genotypes are conventionally represented with a math-like notation, in which genes carried by homologous chromosomes are written on both sides of a fraction bar.1

In order to ease typesetting of fly genotypes in LaTeX documents, I wrote a small LaTeX package, flygenet. This package provides a \genotype macro allowing to write a genotype using a lighter syntax than LaTeX math-mode macros.

For example, instead of writing

$$
\frac{w\ hira^{HR1(floxed)}}{FM7h}; \frac{P\{w^+\ His2Av-mRFP1\} P\{v^+\ hs-I-CreI.R\}}{TM6,Tb\ Hu}
$$

in pure LaTeX, with the \genotype macro one can simply write, for a similar result:

\genotype{w hira^{HR1(floxed)}/FM7h; P\{w^+ His2Av-mRFP1\} P\{v^+ hs-I-CreI.R\}/TM6,Tb Hu}
Examples of flygenet genotypes
Code Result
\genotype{f; cn bw; TM2/Tra}
\genotype{C(1)RM, y^2/Y; In(2LR)O, Cy/Sco; ci^D/ey^D}
\males{nd/Y} \times \virgins{FM7a; In(2LR)O, Cy/Sco}
\virgins{In(2LR)O, Cy/+; TM3, Ser/ftz}
\times
\males{Sco/eve; TM6, Ubx/+}
\virgins{w; In(2LR)O, Cy/odd; P\{w^+ odd^+\}/+}
\times
\males{w/Y; In(2LR)O, Cy/odd; P\{w^+ odd^+\}/+}

The latest released version of the package can be found here:

flygenet-0.3.tar.gz (application/x-gzip, 268K)

And the latest code can always be found in the Git repository, also clonable with the following command:

$ git clone git://git.incenp.org/flygenet.git
  1. Refer to FlyBase for more details on fly genetics nomenclature.