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http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Proper citation: Chemtool (RRID:SCR_023992) Copy
http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/
Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.
Proper citation: ChromImpute (RRID:SCR_023990) Copy
Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
Proper citation: Insight Toolkit (RRID:SCR_024040) Copy
https://github.com/HadrienG/InSilicoSeq
Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
Proper citation: InSilicoSeq (RRID:SCR_024041) Copy
Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer.
Proper citation: Entangle (RRID:SCR_024015) Copy
https://github.com/fccoelho/epigrass
Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.
Proper citation: Epigrass (RRID:SCR_024016) Copy
https://github.com/jnktsj/DNApi/
Software de novo adapter prediction algorithm for small RNA sequencing data.
Proper citation: DNApi (RRID:SCR_024009) Copy
https://www.teuniz.net/edfbrowser/
Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc.
Proper citation: EDFbrowser (RRID:SCR_024021) Copy
Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome.
Proper citation: Assemblytics (RRID:SCR_023967) Copy
https://sourceforge.net/projects/ffp-phylogeny/
Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison.
Proper citation: FFP (RRID:SCR_024018) Copy
https://github.com/danielhuson/dendroscope3
Software Java program for analyzing and visualizing rooted phylogenetic trees and networks.
Proper citation: Dendroscope3 (RRID:SCR_024003) Copy
https://bitbucket.org/genomicepidemiology/kma/src/master/
Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands.
Proper citation: KMA (RRID:SCR_024054) Copy
https://posit.co/products/open-source/shinyserver/
Open Source platform to host multiple Shiny applications on single server.
Proper citation: shiny-server (RRID:SCR_024334) Copy
Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods.
Proper citation: PLAST (RRID:SCR_024170) Copy
https://github.com/ahmedmoustafa/JAligner
Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model.
Proper citation: JAligner (RRID:SCR_024050) Copy
https://seqan.github.io/lambda/
Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.
Proper citation: Lambda (RRID:SCR_024052) Copy
https://github.com/cboursnell/crb-blast
Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
Proper citation: crb-blast (RRID:SCR_024325) Copy
https://www.tau.ac.il/~itaymay/cp/rate4site.html
Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins.
Proper citation: Rate4Site (RRID:SCR_024222) Copy
Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern.
Proper citation: spaced (RRID:SCR_024345) Copy
Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.
Proper citation: Logol (RRID:SCR_024104) Copy
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