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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
https://github.com/SciLifeLab/facs
Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.
Proper citation: FACS (RRID:SCR_000055) Copy
http://compbio.berkeley.edu/proj/juncbase/Home.html
Software used to identify and classify alternative splicing events from RNA-Seq data. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples.
Proper citation: JuncBASE (RRID:SCR_003103) Copy
http://deweylab.biostat.wisc.edu/rsem/
Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.
Proper citation: RSEM (RRID:SCR_000262) Copy
A C++ application designed for compression of genome collections from the same species.
Proper citation: GDC (RRID:SCR_001007) Copy
https://cran.r-project.org/web/packages/phytools/index.html
Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.
Proper citation: phytools (RRID:SCR_015502) Copy
https://github.com/princelab/mspire-simulator
A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components.
Proper citation: Mspire-Simulator (RRID:SCR_001431) Copy
https://github.com/johnlees/seer
Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria.
Proper citation: SEER (RRID:SCR_015499) Copy
http://cbcb.umd.edu/software/metAMOS
A modular and open source metagenomic assembly and analysis pipeline.
Proper citation: MetAMOS (RRID:SCR_011914) Copy
http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.
Proper citation: Cufflinks (RRID:SCR_014597) Copy
http://aebruno.github.io/fusim/
A software tool for simulating fusion transcripts from a reference genome.
Proper citation: FUSIM (RRID:SCR_001015) Copy
https://github.com/broadinstitute/pilon/
Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.
Proper citation: Pilon (RRID:SCR_014731) Copy
http://darwin.uvigo.es/software/prottest_server.html
Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ProtTest (RRID:SCR_014628) Copy
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