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http://pbil.univ-lyon1.fr/software/phyldog/

Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously.

Proper citation: PHYLDOG (RRID:SCR_024487) Copy   

•   Source: SciCrunch Registry

https://github.com/chaoszhang/A-pro

Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.

Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy   

•   Source: SciCrunch Registry

https://kmplot.com/analysis/

Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.

Proper citation: Kaplan Meier Plotter (RRID:SCR_024521) Copy   

•   Source: SciCrunch Registry

https://www.jenoptik.com/products/cameras-and-imaging-modules/microscope-cameras/progres-usb-20-firewire/software-download-progres

Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.

Proper citation: ProgRes Capture Pro (RRID:SCR_024489) Copy   

•   Source: SciCrunch Registry

http://madoka.denglab.org/

Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.

Proper citation: MADOKA (RRID:SCR_024522) Copy   

•   Source: SciCrunch Registry

https://cab.spbu.ru/software/spades/

Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPAdes (RRID:SCR_000131) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.

Proper citation: BLASTP (RRID:SCR_001010) Copy   

•   Source: SciCrunch Registry

http://www.drive5.com/muscle/prefab.htm

Downloadable data designed for testing multiple sequence alignment methods.

Proper citation: PREFAB (RRID:SCR_001009) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/tools/primer-blast/

A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications.

Proper citation: Primer-BLAST (RRID:SCR_003095) Copy   

•   Source: SciCrunch Registry

https://web.stanford.edu/group/pritchardlab/structure.html

Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms.

Proper citation: STRUCTURE (RRID:SCR_017637) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/argus/

Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.

Proper citation: Argus (RRID:SCR_021585) Copy   

•   Source: SciCrunch Registry

https://www.syngene.com/software/genetools-automatic-image-analysis/

Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.

Proper citation: GeneTools (RRID:SCR_022505) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=riskRegression

Software R package provides risk regression models and prediction scores for survival analysis with competing risks.

Proper citation: riskRegression (RRID:SCR_024424) Copy   

•   Source: SciCrunch Registry

https://github.com/SouthGreenPlatform/rap-green

Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package.

Proper citation: RapGreen (RRID:SCR_024426) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ROCit

Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot.

Proper citation: ROCit (RRID:SCR_024420) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=rgdal

Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats.

Proper citation: Rgdal (RRID:SCR_024422) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=survivalROC

Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data.

Proper citation: survivalROC (RRID:SCR_024415) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ggridges

Software R package enables creation of Ridgeline plots in 'ggplot2'

Proper citation: ggridges (RRID:SCR_024511) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gamm4

Software R package to estimate generalized additive mixed models.

Proper citation: gamm4 (RRID:SCR_024507) Copy   

•   Source: SciCrunch Registry

https://ice.synthego.com/#/

Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data.

Proper citation: Inference of CRISPR Edits (RRID:SCR_024508) Copy   

•   Source: SciCrunch Registry