Population Genetics and Cytogenetics Group (XB2)

Departamento de Bioquímica, Genética e Inmunología
Área de Genética. Universidad de Vigo

 

 

 

 

 

 

AFLPMax
AFLPMax is a program aimed at finding the optimal number of AFLP (Amplified Fragment Length Polymorphism, Vos et al. 1995) sampled bands needed to reconstruct an accurate and well-supported AFLP-based phylogeny. Given a reference tree obtained a priori by any phylogenetic inference method and any source of information, AFLPMax provides the optimal number of AFLP bands that would be needed to reconstruct that tree with accuracy and, therefore, it is a tool useful to optimize resources and work for the reconstruction. Further details are explained in Garcia_Pereira et al. AFLPMax: a user-friendly application for computing the optimal number of AFLP markers needed in phylogenetic reconstruction. Molecular Ecology Resources: In Press.

 

ANOVA
Software in compiled BASIC developed to calculate unweighted one way anova for t treatments and n replicates within treatment. The program calculates the probability of getting an observed F ratio significantly larger than the F ratio after X randomizations as well as the parametric anova. The Zip file (from WINZIP 7.0) provides the compiled programs and two files (brun20.lib and brun20.exe) which must be in the same directory than the executable file (anova.exe). Further details are explained in Erlandsson, J., Rolán-Alvarez, E. & Johannesson, K. 1998. Migratory differences between ecotypes of the snail Littorina saxatilis on Galician rocky shores. Evol. Ecol.12: 913-924.

 

FAMSPHERE
FamSphere is a easy to use C++ computer program that implements a distance-based method to allocate families based on co-dominant molecular marker information. Further details are explained in Carvajal-Rodriguez 2007. FamSphere: A computer program for parental allocation from known genotypic pools. Molecular Ecology Notes 7:213-216.

 

JMATING
Software to calculate in an easy and intuitive way the most important sexual isolation and sexual selection estimates. To cite JMating: Antonio Carvajal-Rodríguez and Emilio Rolán-Alvarez 2006 BMC Evolutionary Biology 6: 40. JMating computes the index of pair sexual isolation (Ipsi, Rolán-Alvarez and Caballero 2000: Evolution 54(1):30-36). It also allows for efficient bootstrapping of the estimators for testing hypothesis about sexual selection and isolation. For a comparison of the different statistics for estimating sexual selection see Pérez-Figueroa, A., Caballero, A. and Rolán-Alvarez, E. 2005: Biological Journal of the Linnean Society 85  (3): 307-318).

 

Metapop
Metapop is a software for management of subdivided populations in conservation programs. Using molecular marker data or pedigree information, the software determines the optimal contributions (i.e. number of offspring) of each individual, the number of migrants, and the particular subpopulations involved in the exchange of individuals in order to maintain the largest level of gene diversity in the whole population with a desired control in the rate of inbreeding. Restrictions can be introduced for the total number of migrants, and the mating of particular pairs and their contribution. A full genetic diversity analysis of the population is also carried out. Conservation Genetics (In press).

 

SGoF+
Software to calculate the multitest adjustment probability for Sequential Bonferroni, Benjamini-Hochberg, SGoF and SGoF+ methods. SGoF method is a new multitest adjustment, based on a sequential goodness of fit (SGoF) metatest applied on a probability list previously ranked. SGoF+ is an improvement over SGoF which incorporates a Kolmogorov-Smirnov test to maximize the power of the metatest. Noteworthy, SGoF and SGoF+ increase their statistical power when the number of tests increases. SGoF and SGoF+ metatests can be a valuable alternative for multitest adjustments with high-dimensional biological data. Under plausible biological conditions they can show a statistical power up to two orders of magnitude higher than the Bonferroni and Benjamini-Hochberg adjustments without increasing appreciably the rate of false discoveriers.

 

 

 

 

 

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