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https://omictools.com/splicing-express-tool

Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems.

Proper citation: Splicing Express (RRID:SCR_016498) Copy   

•   Source: SciCrunch Registry

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

Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.

Proper citation: mlgt (RRID:SCR_001211) Copy   

•   Source: SciCrunch Registry

http://pyro.cme.msu.edu/

Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available.

Proper citation: RDPipeline (RRID:SCR_001192) Copy   

•   Source: SciCrunch Registry

http://www.plantagora.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies.

Proper citation: Plantagora (RRID:SCR_001227) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.avadis-ngs.com

Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible,

Proper citation: Avadis (RRID:SCR_000644) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/metavar/

Software package that enables detection of sequence variation between metagenomic samples.

Proper citation: MaryGold (RRID:SCR_000528) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/projects/maia/index.php

Software package for automatic processing of the one- and two- (typically, Cy3-green/Cy5-red) color images produced in cDNA, CGH (comparative genome hybridization) or protein microarray technologies. It incorporates the following modules: * The spot localization module (i) identifies the position of each spot on the array, so that the name of the spotted clone can be associated with the correspondent spot; and (ii) establishes the borders between the neighborhood spots letting one to perform further data processing procedures (i.e. to extract quantitative information) for each spot independently of the other neighborhood spots. Visually this results in the generation of a grid covering the image. The spot localization algorithm is fully automatic and robust with respect to deviations from perfect spot alignment and contamination. As an input, it requires only the common array design parameters: number of blocks and number of spots in the x and y directions of the array. * The spot quantification module for one-color images performs segmentation of the spots and estimates the averaged spot and local background intensities. The spot quantification module for two-color images estimates the ratio of the measured intensities in the two color channels at each spot reflecting differential gene (cDNA technology) or protein expression or a change in DNA copy number (CGH experiments) between the test and control samples for the corresponding gene. This module includes algorithms based on the linear regression and segmentation of the spots. A special procedure for detection and removal of the aberrant pixels has been developed to make ratio estimates more resistant to array contamination. It ensures more consistent ratio estimates obtained from different algorithms, and allows delivery of a single trustable ratio value. * The quality control module provides a value of spot quality reflecting the level of confidence in the obtained quantitative estimates at each spot. These quality values can be used either directly to flag out some spots with the quality lower than the user-defined threshold, or in the follow-up analysis as a weight controlling the contribution/influence of the obtained ratio estimates. The unique spot quality value for a spot is derived from a set of marginal quality parameters characterizing certain features of the spot. The contribution of each quality parameter in the overall quality is automatically evaluated based on the user visual classification of the spots, or using information available from the replicated spots, located at the same array or over a set of replicated arrays. * The image simulator allows the generation of a broad spectrum of microarray images with different types of contamination (like non-specific hybridization and dust) and noise. Since in simulation experiment the true values of the ratios are known exactly, it allows one to evaluate, to test and to compare different algorithms for microarray image processing objectively.

Proper citation: MAIA (Microarray Image Analysis) (RRID:SCR_002239) Copy   

•   Source: SciCrunch Registry

https://github.com/gt1/biobambam

Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

Proper citation: biobambam (RRID:SCR_003308) Copy   

•   Source: SciCrunch Registry

http://hannonlab.cshl.edu/fastx_toolkit/

Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Proper citation: FASTX-Toolkit (RRID:SCR_005534) Copy   

•   Source: SciCrunch Registry

https://github.com/najoshi/sickle

Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read.

Proper citation: Sickle (RRID:SCR_006800) Copy   

•   Source: SciCrunch Registry

http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/

Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible

Proper citation: STRAP (RRID:SCR_005675) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soap3.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. GPU-based software for aligning short reads with a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 3.

Proper citation: SOAP3 (RRID:SCR_005502) Copy   

•   Source: SciCrunch Registry

http://master.bioconductor.org/packages/2.13/bioc/html/BHC.html

Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets.

Proper citation: BHC (RRID:SCR_006399) Copy   

•   Source: SciCrunch Registry

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

A software application for viewing and processing DNA sequencing chromatograms (trace files) that makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. SeqTrace also includes a full-featured trace file viewer and editor. You can view your sequencing chromatograms at a variety of scales and zoom levels, simultaneously view matching forward and reverse traces, edit the called bases, and export individual DNA sequences as well as forward/reverse alignments. SeqTrace supports popular trace file formats, including ABIF, SCF, and ZTR.

Proper citation: SeqTrace (RRID:SCR_005580) Copy   

•   Source: SciCrunch Registry

http://www.biojava.org

Project dedicated to providing Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. Sponsor: BioJava is not formally funded by any grants. Through the OBF they have received sponsorship from Sun Microsystems, Apple Computers and NESCent. The initial development of the phylogenetics module was undertaken as a Google Summer of Code 2007 project in collaboration with NESCent.

Proper citation: BioJava Project (RRID:SCR_007180) Copy   

•   Source: SciCrunch Registry

http://www.iqtree.org

Software tool for phylogenomic inference.

Proper citation: IQ TREE (RRID:SCR_021163) Copy   

•   Source: SciCrunch Registry

https://qiime2.org/

Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities.

Proper citation: QIIME2 (RRID:SCR_021258) Copy   

•   Source: SciCrunch Registry

https://omictools.com/ecgene-tool

Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.

Proper citation: ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) Copy   

•   Source: SciCrunch Registry

http://driverdb.ym.edu.tw/DriverDB/intranet/init.do

A database for cancer driver gene/mutation that incorporates a huge amount of exome-seq data, annotation databases (such as dbSNP, 1000 Genome and Cosmic), and published bioinformatics algorithms dedicated to driver gene/mutation identification.

Proper citation: DriverDB (RRID:SCR_007736) Copy   

•   Source: SciCrunch Registry

http://nectarmutation.org/main

A database and web application to annotate disease-related and functionally important amino acids in human proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NECTAR (RRID:SCR_007757) Copy   

•   Source: SciCrunch Registry