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https://sites.google.com/site/beckerjeremie/home/nucleofinder
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
Proper citation: NucleoFinder (RRID:SCR_000368) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
http://proteinprophet.sourceforge.net/
Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.
Proper citation: ProteinProphet (RRID:SCR_000286) Copy
https://github.com/mickaelleclercq/mirdup
A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA.
Proper citation: MiRdup (RRID:SCR_000316) Copy
http://www.bioconductor.org/packages/release/bioc/html/QUALIFIER.html
Software that provides quality control and quality assessment tools for gated flow cytometry data.
Proper citation: QUALIFIER (RRID:SCR_000389) Copy
http://sourceforge.net/projects/fqzcomp/
A basic fastq compressor, designed primarily for high performance.
Proper citation: fqzcomp (RRID:SCR_000299) Copy
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
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
http://sourceforge.net/projects/hlaseq/
An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.
Proper citation: HLASeq (RRID:SCR_004185) Copy
http://pass.cribi.unipd.it/cgi-bin/pass.pl
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Proper citation: PASS-bis (RRID:SCR_004176) Copy
http://www.cs.gsu.edu/~serghei/?q=drut
Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data.
Proper citation: DRUT (RRID:SCR_004351) Copy
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
http://compbio.cs.wayne.edu/software/squeezambler/
Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells.
Proper citation: Squeezambler (RRID:SCR_004385) Copy
Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.
Proper citation: SNiPer-HD (RRID:SCR_004383) Copy
http://sourceforge.net/projects/vanator-cvr/
A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.
Proper citation: Vanator (RRID:SCR_004370) Copy
http://www.csd.uwo.ca/~ilie/BOND/
Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs.
Proper citation: Basic OligoNucleotide Design (RRID:SCR_004492) Copy
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/
Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOrt-ITEMS (RRID:SCR_004716) Copy
A multiple-sample, technology-aware SNP and indel caller.
Proper citation: UnifiedGenotyper (RRID:SCR_004710) Copy
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075146
An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.
Proper citation: NuChart (RRID:SCR_004703) Copy
http://matsen.fhcrc.org/pplacer/
Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
Proper citation: Pplacer (RRID:SCR_004737) Copy
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