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http://kmersvm.beerlab.org/

A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.

Proper citation: kmer-SVM (RRID:SCR_010882) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.au.tsinghua.edu.cn/software/NURD/

An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NURD (RRID:SCR_010988) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/Tools/msa/kalign/

A fast and accurate multiple sequence alignment algorithm.

Proper citation: Kalign (RRID:SCR_011810) Copy   

•   Source: SciCrunch Registry
  

http://mafft.cbrc.jp/alignment/server/

Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.

Proper citation: MAFFT (RRID:SCR_011811) Copy   

•   Source: SciCrunch Registry
  

http://wishart.biology.ualberta.ca/cgview/

A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CGView (RRID:SCR_011779) Copy   

•   Source: SciCrunch Registry
  

http://bioen-compbio.bioen.illinois.edu/PSAR-Align/

Software for improving multiple sequence alignment using probabilistic sampling.

Proper citation: PSAR-Align (RRID:SCR_011814) Copy   

•   Source: SciCrunch Registry
  

http://gaggle.systemsbiology.net/docs/geese/genomebrowser/

An open source software tool for visualizing high-density data plotted against coordinates on the genome.

Proper citation: Gaggle (RRID:SCR_011780) Copy   

•   Source: SciCrunch Registry
  

https://bioinf.eva.mpg.de/patman/

Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PatMaN (RRID:SCR_011821) Copy   

•   Source: SciCrunch Registry
  

http://www.g-language.org/GenomeProjector/

A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.

Proper citation: Genome Projector (RRID:SCR_011790) Copy   

•   Source: SciCrunch Registry
  

http://utgenome.org/index.html

An open-source software for developing personalized genome browsers that work in web browsers.

Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy   

•   Source: SciCrunch Registry
  

http://graphics.med.yale.edu/trim/

A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.

Proper citation: Btrim (RRID:SCR_011836) Copy   

•   Source: SciCrunch Registry
  

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

Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: cutadapt (RRID:SCR_011841) Copy   

•   Source: SciCrunch Registry
  

http://genopole.pasteur.fr/SynTView/

An interactive multi-view genome browser for next-generation comparative microorganism genomics.

Proper citation: SynTView (RRID:SCR_011939) Copy   

•   Source: SciCrunch Registry
  

http://ccb.jhu.edu/software/glimmer/index.shtml

A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

Proper citation: Glimmer (RRID:SCR_011931) Copy   

•   Source: SciCrunch Registry
  

http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php

A Next-Generation Sequencing Simulator for Metagenomics.

Proper citation: NeSSM (RRID:SCR_011941) Copy   

•   Source: SciCrunch Registry
  

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