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http://evolution.genetics.washington.edu/lamarc/lamarc_prog.html

Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software)

Proper citation: LAMARC (RRID:SCR_009252) Copy   

•   Source: SciCrunch Registry

http://www.math.mtu.edu/~shuzhang/software.html

Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software)

Proper citation: HS-TDT (RRID:SCR_009240) Copy   

•   Source: SciCrunch Registry

http://research.nhgri.nih.gov/ROMPrev/

Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software)

Proper citation: ROMPREV (RRID:SCR_009361) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/simulate.html

Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software)

Proper citation: SIMULATE (RRID:SCR_009391) Copy   

•   Source: SciCrunch Registry

http://www.unc.edu/~yunmli/MaCH-Admix/

A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix.

Proper citation: MaCH-Admix (RRID:SCR_009598) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry

http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software)

Proper citation: SASQUANT (RRID:SCR_013122) Copy   

•   Source: SciCrunch Registry

http://www.aps.uoguelph.ca/~msargol/qmsim/

Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software)

Proper citation: QMSIM (RRID:SCR_013123) Copy   

•   Source: SciCrunch Registry

http://perlprimer.sourceforge.net/

A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.

Proper citation: PerlPrimer (RRID:SCR_012038) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/BoolNet/index.html

Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks.

Proper citation: BoolNet (RRID:SCR_024264) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/cmprsk/index.html

Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks.

Proper citation: cmprsk (RRID:SCR_024265) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/bio3d/index.html

Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data.

Proper citation: bio3d (RRID:SCR_024266) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/DoseFinding/index.html

Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology.

Proper citation: DoseFinding (RRID:SCR_024268) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/distory/index.html

Software R package for geodesic distance between phylogenetic trees and associated functions.

Proper citation: distory (RRID:SCR_024269) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/alakazam/index.html

Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage.

Proper citation: alakazam (RRID:SCR_024261) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ade4/index.html

Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table.

Proper citation: ade4 (RRID:SCR_024259) Copy   

•   Source: SciCrunch Registry

https://psignifit.sourceforge.net/

Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.

Proper citation: psignifit (RRID:SCR_024196) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html

Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

Proper citation: bridgedbr (RRID:SCR_024231) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/CNEr/

Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements.

Proper citation: CNEr (RRID:SCR_024233) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/GenomeInfoDb/

Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order.

Proper citation: genomeinfodb (RRID:SCR_024235) Copy   

•   Source: SciCrunch Registry