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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://phenoscape.org/

Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions.

Proper citation: Phenoscape (RRID:SCR_003799) 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://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.atgc-montpellier.fr/phyml/

Web phylogeny server based on the maximum-likelihood principle.

Proper citation: PhyML (RRID:SCR_014629) Copy   

•   Source: SciCrunch Registry

http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder

A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis.

Proper citation: QmRLFS-finder (RRID:SCR_014584) Copy   

•   Source: SciCrunch Registry

http://www.funrich.org/

A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts.

Proper citation: FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) Copy   

•   Source: SciCrunch Registry

http://multiqc.info/

Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.

Proper citation: MultiQC (RRID:SCR_014982) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/octave/

A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments. It may also be used as a batch-oriented language. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, functions written in the Octave language, or by using dynamically loaded modules written in C, C++, Fortran, or other languages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GNU Octave (RRID:SCR_014398) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/topGO.html

Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Proper citation: topGO (RRID:SCR_014798) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/danposdoc/

Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing.

Proper citation: DANPOS2 (RRID:SCR_015527) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

http://abacas.sourceforge.net

Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.

Proper citation: ABACAS (RRID:SCR_015852) Copy   

•   Source: SciCrunch Registry

http://myriads.webs.uvigo.es/

Software package for p value based multiple testing that also implements dependence test and p-value simulation.

Proper citation: Myriads (RRID:SCR_017447) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX

Software for protein domain search. It is a part of Embassy software package.

Proper citation: DOMAINATRIX (RRID:SCR_016084) Copy   

•   Source: SciCrunch Registry

https://git.metabarcoding.org/obitools/ecopcr/wikis/home

Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Ecopcr (RRID:SCR_016082) Copy   

•   Source: SciCrunch Registry

https://github.com/rbutleriii/Clinotator

Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics.

Proper citation: Clinotator (RRID:SCR_016054) Copy   

•   Source: SciCrunch Registry