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https://dalexander.github.io/admixture/download.html

A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ADMIXTURE (RRID:SCR_001263) Copy   

•   Source: SciCrunch Registry

http://med.stanford.edu/tanglab/software/frappe.html

Software using a f frequentist approach for estimating individual ancestry proportion.

Proper citation: frappe (RRID:SCR_001264) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/pindel/0.2.4/

Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Pindel (RRID:SCR_000560) Copy   

•   Source: SciCrunch Registry

http://paleogenomics.irmacs.sfu.ca/FPSAC/

Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.

Proper citation: FPSAC (RRID:SCR_000555) Copy   

•   Source: SciCrunch Registry

http://genome.crg.es/software/gfftools/GFF2PS.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.

Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy   

•   Source: SciCrunch Registry

http://www.brown.edu/Research/Istrail_Lab/hapcompass.php

Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings.

Proper citation: HapCompass (RRID:SCR_000942) Copy   

•   Source: SciCrunch Registry

http://www.biobase-international.com/product/genome-trax

Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia.

Proper citation: Genome Trax (RRID:SCR_001234) Copy   

•   Source: SciCrunch Registry

http://www.zbh.uni-hamburg.de/?id=211

A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases.

Proper citation: TALLYMER (RRID:SCR_001244) Copy   

•   Source: SciCrunch Registry

http://www.iro.umontreal.ca/~csuros/quadgt/

Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

Proper citation: QuadGT (RRID:SCR_000073) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

Proper citation: SOAPfuse (RRID:SCR_000078) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/edgebio

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider.

Proper citation: EdgeBio (RRID:SCR_000183) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development

A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

Proper citation: ARACHNE (RRID:SCR_000351) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/genomics-services-lab

A lab that offers genetic research tools such as RNA sequencing and a variety of arrays.

Proper citation: HudsonAlpha Genomics Services Lab (RRID:SCR_000353) Copy   

•   Source: SciCrunch Registry

http://www.biomol-informatics.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 12, 2021. Technology based company in Madrid that offers consulting services on Bioinformatics in areas of research, diagnostics and pharmaceutical industry.

Proper citation: Biomol-Informatics (RRID:SCR_004081) Copy   

•   Source: SciCrunch Registry

http://genomics.princeton.edu/AndolfattoLab/MSG.html

A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.

Proper citation: MSG (RRID:SCR_004161) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/perm/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Proper citation: PerM (RRID:SCR_004223) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/act/

A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

Proper citation: ACT: Artemis Comparison Tool (RRID:SCR_004507) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.sfu.ca/software-variation-hunter

A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.

Proper citation: VariationHunter (RRID:SCR_004865) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/phymm/

Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.

Proper citation: Phymm and PhymmBL (RRID:SCR_004751) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/destruct/

A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.

Proper citation: deStruct (RRID:SCR_004747) Copy   

•   Source: SciCrunch Registry