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https://scicrunch.org/scicrunch/data/source/nlx_154697-10/search?q=*&l=

A virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS).

Proper citation: Integrated Software (RRID:SCR_004745) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/maia-1.0/

Software package of programs for complex segregation analysis in animal pedigrees.

Proper citation: MAIA (RRID:SCR_007153) Copy   

•   Source: SciCrunch Registry

http://claire.bardel.free.fr/software.html

Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci.

Proper citation: ALTree (RRID:SCR_007562) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/

Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAP (RRID:SCR_000689) Copy   

•   Source: SciCrunch Registry

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

Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)

Proper citation: LDHEATMAP (RRID:SCR_006312) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/alkes-price/software/

Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software)

Proper citation: Hapmix (RRID:SCR_004203) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/fdudbridge/software/pelican

Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.

Proper citation: PELICAN (RRID:SCR_001695) Copy   

•   Source: SciCrunch Registry

http://wwwchg.duhs.duke.edu/research/osa.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.

Proper citation: OSA (RRID:SCR_002016) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu//abecasis/Metal/

Software application designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. (entry from Genetic Analysis Software)

Proper citation: METAL (RRID:SCR_002013) Copy   

•   Source: SciCrunch Registry

http://www.omicsexpress.com/sva.php

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.

Proper citation: SVA (RRID:SCR_002155) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ldb;

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application that integrate genetic linkage map and physical map (entry from Genetic Analysis Software)

Proper citation: LDB/LDB+ (RRID:SCR_000839) Copy   

•   Source: SciCrunch Registry

http://research.calit2.net/hap/

Software application (entry from Genetic Analysis Software)

Proper citation: HAP 1 (RRID:SCR_000837) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LAMBDAA (RRID:SCR_001128) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/carol

Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.

Proper citation: CAROL (RRID:SCR_001800) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LDMET (RRID:SCR_001127) Copy   

•   Source: SciCrunch Registry

http://www.biostat.harvard.edu/complab/dchip/snp.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: DCHIP LINKAGE (RRID:SCR_000835) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/floss/floss.htm

Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software)

Proper citation: FLOSS (RRID:SCR_000836) Copy   

•   Source: SciCrunch Registry

http://support.illumina.com/sequencing/sequencing_software/casava.html

Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting

Proper citation: CASAVA (RRID:SCR_001802) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Polymutt

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)

Proper citation: POLYMUTT (RRID:SCR_002051) Copy   

•   Source: SciCrunch Registry