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http://metavelvet.dna.bio.keio.ac.jp/

Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet.

Proper citation: MetaVelvet (RRID:SCR_011915) Copy   

•   Source: SciCrunch Registry
  

http://omics.informatics.indiana.edu/GeneStitch/

Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.

Proper citation: GeneStitch (RRID:SCR_011910) Copy   

•   Source: SciCrunch Registry
  

http://www.jcvi.org/metarep/

A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.

Proper citation: METAREP (RRID:SCR_011926) Copy   

•   Source: SciCrunch Registry
  

http://bayescall.sourceforge.net/

An efficient model-based base-calling algorithm for high-throughput sequencing.

Proper citation: naiveBayesCall (RRID:SCR_011866) Copy   

•   Source: SciCrunch Registry
  

http://pages.cs.wisc.edu/~bsettles/abner/

A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.

Proper citation: ABNER (RRID:SCR_011868) Copy   

•   Source: SciCrunch Registry
  

http://transcriptome.ens.fr/eoulsan/

A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.

Proper citation: Eoulsan (RRID:SCR_011901) Copy   

•   Source: SciCrunch Registry
  

http://www.litinspector.org/

A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.

Proper citation: LitInspector (RRID:SCR_011870) Copy   

•   Source: SciCrunch Registry
  

http://vina.scripps.edu/

An open-source program for doing molecular docking.

Proper citation: AutoDock Vina (RRID:SCR_011958) Copy   

•   Source: SciCrunch Registry
  

http://cran.r-project.org/web/packages/vegan/index.html

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Proper citation: vegan (RRID:SCR_011950) Copy   

•   Source: SciCrunch Registry
  

http://opm.phar.umich.edu/

Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal.

Proper citation: Orientations of Proteins in Membranes database (RRID:SCR_011961) Copy   

•   Source: SciCrunch Registry
  

http://scalpel.sourceforge.net/

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).

Proper citation: Scalpel (RRID:SCR_012107) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mtoolbox/

Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.

Proper citation: MToolBox (RRID:SCR_012112) Copy   

•   Source: SciCrunch Registry
  

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

A user-friendly software tool to estimate allele-specific gene expression.

Proper citation: Allim (RRID:SCR_012114) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/snpratiotest/

Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.

Proper citation: SNP ratio test (RRID:SCR_012070) Copy   

•   Source: SciCrunch Registry
  

https://code.google.com/p/compomics-utilities/

A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics.

Proper citation: compomics-utilities (RRID:SCR_012073) Copy   

•   Source: SciCrunch Registry
  

https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/

Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms.

Proper citation: NetNGlyc (RRID:SCR_001570) Copy   

•   Source: SciCrunch Registry
  

https://services.healthtech.dtu.dk/services/YinOYang-1.2/

Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms.

Proper citation: YinOYang (RRID:SCR_001605) Copy   

•   Source: SciCrunch Registry
  

https://www.ebi.ac.uk/jdispatcher/msa/clustalo?stype=protein

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

Proper citation: Clustal Omega (RRID:SCR_001591) Copy   

•   Source: SciCrunch Registry
  

http://bios.unc.edu/~weisun/software/asSeq.htm

Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq

Proper citation: asSeq (RRID:SCR_001625) Copy   

•   Source: SciCrunch Registry
  

https://github.com/uci-cbcl/PyLOH

Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework.

Proper citation: PyLOH (RRID:SCR_001511) Copy   

•   Source: SciCrunch Registry