SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recombining region within which a single bi-allelic site has experienced natural selection. SelSim allows simulation from either a fully stochastic model of, or deterministic approximations to, natural selection within a coalescent framework. A number of different mutation models are available for simulating surrounding neutral variation. The package enables a detailed exploration of the effects of different models and strengths of selection on patterns of diversity.
OrthoSelect is a easy-to-install and easy-to-use tool for finding ortholog groups in EST databases. It automatically searches assembled EST sequences against databases of ortholog groups (OG), assigns ESTs to these pre-defined OGs, translates the sequences into proteins, eliminates redundant sequences assigned to the same OG, creates multiple sequence alignments of identified ortholog sequences and others the possibility to further process this alignment in a last step. OrthoSelect performes better than the best-hit selection strategy and shows reliable results re-annotating database member sequences of OrthoMCL-DB and KOG. Since a correct orthology assignment is a important prerequisite for the construction of reliable data sets, OrthoSelect is capable of producing such data sets. This makes a OrthoSelect a valuable tool for researcher dealing with large EST libraries focussing on constructing data sets for phylogenetic reconstructions.
Alexa Fluor® Selection Guide widget is designed to provide you with a concise and informative set of criteria for choosing the optimal Alexa Fluor® dye for your antibody or protein labeling application. Each page in this guide highlights a different Alexa Fluor® dye by summarizing key spectral data, excitation sources, and relevant product offerings. Full excitation and emission spectra are included for each of the dyes.
G-POT is a primer set selection tool that minimizes the number of primers needed to amplify a set of loci while ensuring that each locus is amplified by a pair of primers located within L basepairs of each other, where L is an input parameter.
PRIMER-ILP is a primer set selection tool that minimizes the number of primers needed to amplify a set of loci while ensuring that each locus is amplified by a pair of primers located within L basepairs of each other, where L is an input parameter. The code uses the mixed integer linear programming solver from the GNU Linear Programming Package (GLPK) to solve the IP problem created from the input target sequences.