LoRTE – detecting transposon-induced genomic variants using low coverage PacBio long read sequences.
Documentation and download: [LoRTE]
Ref: Disdero E., and Filée J. (2017). LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences. Mobile DNA, 8(1), 5. [DOI: 10.1186/s13100-017-0088-x].
Article Recommendation: [F1000Prime]
Quetzal – an Open-source C++ library presenting a set of reusable components for coalescence-based simulation programs design and integration in an ABC framework for parameters estimation.
Documentation: [link on GitHub]
Code repository: [link on GitHub]
devRate – a set of tools to quantify the relationship between development rate and temperature in ectotherms [link on R CRAN].
Ref: Rebaudo F., Struelens Q., Dangles O. (2017) Modeling temperature-dependent development rate and phenology in arthropods: the devRate package for R. Methods in Ecology and Evolution, 00: 1-7. [DOI: 10.1111/2041-210X.12935].
noia – is an implementation for R of the Natural and Orthogonal InterAction model (NOIA), a statistical framework aiming at estimating and manipulating genetic effects of quantitative characters. This page is an informal tutorial describing the practical use of the software, as well as some basic concepts in quantitative genetics modeling: noia-tutorial. [link on R CRAN].
Ref: Le Rouzic A., Alvarez-Castro JM., Carlborg Ö. (2008) Dissection of the genetic architecture of body weight in chicken reveals the impact of epistasis on domestication traits. Genetics, 179(3), 1591-1599. [DOI: 10.1534/genetics.108.089300 ].
simAdapt – an individual-based genetic model for simulating landscape management impacts on populations [link on CoMSES Computational Model Library].
Ref: Rebaudo F., Le Rouzic A., Dupas S., Silvain J.F., Harry M., Dangles O. (2013) SimAdapt: An individual-based genetic model for simulating landscape management impacts on populations. Methods in Ecology and Evolution, 4:595-600. [DOI: 10.1111/2041-210X.12041]