:: DESCRIPTION
GPC is a website for performing power calculations for the design of linkage and association genetic mapping studies of complex traits.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Purcell S, Cherny SS, Sham PC. (2003)
Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits.
Bioinformatics, 19(1):149-150.
:: DESCRIPTION
KIN (Kinship Calculator) includes a driver program and an executable program based on Morgan v2.0/kinship and Werner pedigree example.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
2LD is a simple program calculating linkage disequilibrium (LD) measures between two polymorphic markers.
LDSHELL is a shell program for 2LD
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhao, J. H. (2004)
“2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis“.
Bioinformatics, 20, 1325-1326
Noonan, J.P., Li, J., Nguyen, L., Caolie, C., Dickson, M., Grimwood, J., Schmutz, J., Feldman, M. W., Myers, R. M. (2003),
Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster
Am. J. Hum. Genet.Vol. 72, pp. 621-635.
:: DESCRIPTION
PornStar (Phylogenetics on Rick’s Network) is a group of command-line executables developed for Linux that allow you to; 1) create Paup* maximum likelihood search and bootstrap blocks and 2) perform a series of likelihood ratio tests to determine a “best” fitting model for your data. This part of Pornstar is a complete RIPOFF-HACK (Although all of the code was written from scratch, the idea was stolen) of David Posada’s ModelTest; it even uses the same executable PAUP block file. I have, however, left out any AIC calculations. For further information about the use of models/ model fitting in phylogenetic analysis
::DEVELOPER
the Bell Plant Evolution & Phylogenetics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PGC, the Protein Geometry Calculator, is an interpreter for a simple,expression-based language, resembling GNU bc in its interface, and intended for use in performing calculations related to molecular geometry. While it does not, in itself, provide facilities for performing such calculations, in its current form it provides interfaces for software packages that do; its structure allows data from these packages to be imported, manipulated, and exported for the use of other packages. This manual documents the syntax of the language, the library of functions available to users, and methods for extending this library.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ASP is a power calculator for gene mapping using a sibpair design (concordant or discordant). ASP employs a diallelic model for the trait locus and simulates parental and offspring genotypes under Hardy-Weinberg equilibrium. Marker locus genotypes are simulated conditional upon the inheritance pattern at the trait locus and tested for non-Mendelian ibd sharing. For discordant sibs, an unrestricted likelihood ratio test is used; for affected sibpairs, the power of the dataset is also determined using a restricted likelihood ratio test.
ASPSHARE complements ASP in that it allows rapid calculation of the expected ibd sharing at the trait locus, based upon the model parameters, and the incidence corresponding to the respective parameters. It should therefore be used prior to any time-consuming simulations to assess whether a model is sensibel.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MASKER is a program for calculating solvent accessible surface (SAS) solvent excluded surface (SES) and solvation energy. Three program that use the MASKER module are included in this package:
pdbmask — calculates the solvent excluded surface of atoms in PDB format
maskercm — calculates the pairwise buried surface of residues in a protein
voidmask — finds the locations of buried empty spaces with in a protein, or any molecule.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citaiton
C. Bystroff (2002)
MASKER: Improved solvent excluded molecular surface area estimations using Boolean masks
Protein Engineering, 15:959-965
:: DESCRIPTION
LD50 Calculators can input a tab-delimited text file of surviving mice to caculate LD50 values. LD50 values calculated by Reed-Muench (command-line interface only) or Moving Average Interpolation (graphical interface).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.
If you use the LD50 calculators, please cite:
Kim CC, Monack D, Falkow S.
Modulation of virulence by two acidified nitrite-responsive loci of Salmonella enterica serovar Typhimurium.
Infect Immun. 2003 Jun;71(6):3196-205.
