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https://github.com/ekmolloy/fastmulrfs
Software pipeline for estimating species trees from multi copy gene trees.
Proper citation: FastMulRFS (RRID:SCR_024505) Copy
http://www.cs.cmu.edu/~durand/Notung/
Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses.
Proper citation: NOTUNG (RRID:SCR_024484) Copy
https://CRAN.R-project.org/package=CMplot
Software drawing R package designed for Manhattan plot of genomic analysis.
Proper citation: CMplot (RRID:SCR_024514) Copy
https://github.com/PoisonAlien/Maftools
Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files.
Proper citation: maftools (RRID:SCR_024519) Copy
http://mummer.sourceforge.net/
Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.
Proper citation: MUMmer (RRID:SCR_018171) Copy
Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.
Proper citation: SRAMP (RRID:SCR_024500) Copy
http://rna.tbi.univie.ac.at//cgi-bin/RNAWebSuite/RNAfold.cgi
Web server predict secondary structures of single stranded RNA or DNA sequences.
Proper citation: RNAfold (RRID:SCR_024427) Copy
https://nano-measurer.software.informer.com/
Software tool to process micrograph images for particle size.
Proper citation: Nano Measurer (RRID:SCR_024493) Copy
https://topospro.com/software/
Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters.
Proper citation: ToposPro (RRID:SCR_024496) Copy
https://www.cs.cmu.edu/~jernst/stem/
Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology.
Proper citation: Stem (RRID:SCR_024499) Copy
Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis.
Proper citation: Agilent Seahorse Wave (RRID:SCR_024491) Copy
https://swissmodel.expasy.org/lddt
Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility.
Proper citation: lDDT (RRID:SCR_024524) Copy
http://www.rna-society.org/rnalocate/
Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation.
Proper citation: RNALocate (RRID:SCR_024418) Copy
https://github.com/adamallo/SimPhy
Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees.
Proper citation: SimPhy (RRID:SCR_024501) Copy
http://mutationassessor.org/r3/
Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Mutation Assessor (RRID:SCR_024502) Copy
https://github.com/pinellolab/CRISPResso2
Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.
Proper citation: CRISPResso2 (RRID:SCR_024503) Copy
https://silebat.github.io/FSK-Lab/openbugs.html
Software for analysing complex statistical models using Markov chain Monte Carlo methods.
Proper citation: OpenBUGS (RRID:SCR_024488) Copy
https://github.com/bzhanglab/AutoRT/
Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides.
Proper citation: AutoRT (RRID:SCR_024513) Copy
https://www.reading.ac.uk/bioinf/ModFOLD/
Web server for the global and local quality estimation of 3D protein models
Proper citation: ModFOLD (RRID:SCR_024518) Copy
A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.
Proper citation: Metscape (RRID:SCR_014687) Copy
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