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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HAPMIXMAP Resource Report Resource Website |
HAPMIXMAP (RRID:SCR_006066) | HAPMIXMAP | software application, software resource | Software application for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154391 | SCR_006066 | 2026-08-04 09:41:29 | 0 | |||||||||
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PARENTE Resource Report Resource Website 1+ mentions |
PARENTE (RRID:SCR_004717) | PARENTE | software application, software resource | Software application for parentage inference using molecular data from diploid codominant markers (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154508 | SCR_004717 | 2026-08-04 09:41:12 | 2 | |||||||||
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Multipoint Identical-by-descent Method Resource Report Resource Website |
Multipoint Identical-by-descent Method (RRID:SCR_004676) | MIM | software application, software resource | Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | PMID:9433587 | nlx_154482 | SCR_004676 | 2026-08-04 09:41:11 | 0 | ||||||||
|
PEDRAW/WPEDRAW Resource Report Resource Website |
PEDRAW/WPEDRAW (RRID:SCR_004797) | PEDRAW/WPEDRAW | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A pedigree drawing program using LINKAGE data files (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-dos, ms-windows, x-window | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154527 | SCR_004797 | Pedigree Drawing/ Window Pedigree Drawing (MS-Window and X-Window version of PEDRAW) | 2026-08-04 09:41:13 | 0 | |||||||
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LDHAT Resource Report Resource Website 10+ mentions |
LDHAT (RRID:SCR_006298) | LDHAT | software application, software resource | Software package for the analysis of recombination rates from population genetic data (entry from Genetic Analysis Software) | gene, genetic, genomic, c, dos | is listed by: Genetic Analysis Software | nlx_154423 | SCR_006298 | 2026-08-04 09:41:33 | 45 | |||||||||
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TDTASP Resource Report Resource Website 1+ mentions |
TDTASP (RRID:SCR_004943) | TDTASP | software application, software resource | Software application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran95, unix, ms-windows | is listed by: Genetic Analysis Software | nlx_154675 | SCR_004943 | Power and Sample-Size Calculations for the TDT and ASP Tests | 2026-08-04 09:41:15 | 3 | ||||||||
|
TDT/S-TDT Resource Report Resource Website 1+ mentions |
TDT/S-TDT (RRID:SCR_005548) | TDT/S-TDT | software application, software resource | Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, ms-windows, (95/nt) | is listed by: Genetic Analysis Software | nlx_154679 | SCR_005548 | Transmission Disequilibrium Test and Sib Transmission Disequilibrium Test | 2026-08-04 09:41:23 | 3 | ||||||||
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SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | software application, commercial organization, software resource | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-08-04 09:40:34 | 16 | |||||
|
PEDSCRIPT Resource Report Resource Website |
PEDSCRIPT (RRID:SCR_004571) | PEDSCRIPT | software application, software resource | Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154528 | SCR_004571 | 2026-08-04 09:41:10 | 0 | |||||||||
|
HAPLOBLOCKFINDER Resource Report Resource Website 1+ mentions |
HAPLOBLOCKFINDER (RRID:SCR_005844) | HAPLOBLOCKFINDER | software application, software resource | Software package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine. (entry from Genetic Analysis Software) | gene, genetic, genomic, c and perl, unix, ms-windows | is listed by: Genetic Analysis Software | nlx_154380 | SCR_005844 | 2026-08-04 09:41:27 | 6 | |||||||||
|
POLYMUTT Resource Report Resource Website 1+ mentions |
POLYMUTT (RRID:SCR_002051) | Polymutt | software application, software resource | Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation sequencing, mutation, de novo point mutation, single nucleotide variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:23055937 | Free, Available for download, Freely available | OMICS_00088, nlx_154539 | SCR_002051 | POLYmorphism and de novo MUTaTion call in families with sequencing data | 2026-08-04 09:40:32 | 3 | ||||||
|
PEDPLOT Resource Report Resource Website |
PEDPLOT (RRID:SCR_003843) | PEDPLOT | software application, software resource | Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, postscript, unix, (sparc-solaris 2.5/dec unix 4.0/x86-solaris 2.6) | is listed by: Genetic Analysis Software | nlx_154526 | SCR_003843 | 2026-08-04 09:41:00 | 0 | |||||||||
|
LDMAP Resource Report Resource Website 1+ mentions |
LDMAP (RRID:SCR_006308) | LDMAP | software application, software resource | Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, solaris | is listed by: Genetic Analysis Software | nlx_154425 | SCR_006308 | 2026-08-04 09:41:34 | 8 | |||||||||
|
POPGEN Resource Report Resource Website 100+ mentions |
POPGEN (RRID:SCR_007315) | software application, software resource | An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154543, SCR_009374, nlx_154596 | http://mathgen.stats.ox.ac.uk/software.html, https://cran.r-project.org/web/packages/popgen/index.html | SCR_007315 | R/POPGEN | 2026-08-04 09:41:48 | 198 | ||||||||
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PEDIGREEQUERY Resource Report Resource Website 1+ mentions |
PEDIGREEQUERY (RRID:SCR_009041) | PEDIGREEQUERY | software application, software resource | Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154007, biotools:pedcut | https://bio.tools/pedcut | SCR_009041 | 2026-08-04 09:42:18 | 1 | ||||||||
|
PATH Resource Report Resource Website 100+ mentions |
PATH (RRID:SCR_009042) | PATH | software application, software resource | Web application to investigate gene-gene interactions in genetic association studies designed to: 1. Interface your SNP data with biological information from several online bioinformatics databases. 2. Generate biologically plausible hypotheses for testing gene-gene interactions. 3. Select a subset of SNPs and conduct SNP-SNP interaction tests. 4. Store analysis results. 5. Explore analysis results through interactive plots and summary tables. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, ms-windows, linux, FASEB list | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154015 | SCR_009042 | 2026-08-04 09:42:16 | 253 | ||||||||
|
VarScan Resource Report Resource Website 1000+ mentions |
VarScan (RRID:SCR_006849) | VarScan, VarScan 2 | software application, software resource | Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software). | gene, genetic, genomic, java, illumina, solid, life/pgm, roche/454, next-generation sequencing, variant, mutation caller, exome, whole-genome, snp, copy number alteration, somatic mutation, subclonal mutation, mutation, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is organization facet of: Washington University in St. Louis; Missouri; USA |
PMID:22300766 PMID:19542151 DOI:10.1101/gr.129684.111 |
Free, Available for download, Freely available | , nlx_154687, biotools:varscan, OMICS_00094 | http://varscan.sourceforge.net/, http://dkoboldt.github.io/varscan/, https://bio.tools/varscan, https://sources.debian.org/src/varscan/ | http://genome.wustl.edu/software/varscan, http://tvap.genome.wustl.edu/tools/varscan/ | SCR_006849 | Varscan2, VarScan - variant detection in massively parallel sequencing data, Varscan | 2026-08-04 09:41:43 | 1769 | ||||
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LSP Resource Report The record is no longer available at this source. |
LSP (RRID:SCR_007059) | LSP | software application, software resource | Software application that is part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software) | gene, genetic, genomic, c and pascal, unix, vms, ms-dos, os2 | is listed by: Genetic Analysis Software | SCR_007059 | Linkage Setup Program | 2026-08-04 09:41:45 | 0 | |||||||||
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FASTSLINK Resource Report Resource Website 10+ mentions |
FASTSLINK (RRID:SCR_008664) | FASTSLINK | software application, software resource | Software application that is a faster version of SLINK (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: SLINK is related to: SUP |
nlx_154312, biotools:snpcaller | https://bio.tools/snpcaller | SCR_008664 | faster SLINK | 2026-08-04 09:42:11 | 12 | |||||||
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RTDT Resource Report Resource Website 10+ mentions |
RTDT (RRID:SCR_007336) | RTDT | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, matlab, c++ | is listed by: Genetic Analysis Software | nlx_154579 | SCR_007336 | Robust Transmission/Disequilibrium Test | 2026-08-04 09:41:49 | 17 |
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