Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

http://logol.genouest.org/

Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.

Proper citation: Logol (RRID:SCR_024104) Copy   

•   Source: SciCrunch Registry

http://bioinfo.unl.edu/gramalign.php

Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences.

Proper citation: GramAlign (RRID:SCR_024032) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/rki_bioinformatics/IDeFIX

Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s).

Proper citation: IDeFIX (RRID:SCR_024033) Copy   

•   Source: SciCrunch Registry

https://github.com/lbcb-sci/graphmap2

Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices

Proper citation: GraphMap2 (RRID:SCR_024035) Copy   

•   Source: SciCrunch Registry

https://github.com/genouest/biomaj

Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository.

Proper citation: BioMAJ (RRID:SCR_023983) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/kineticsTools

Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol.

Proper citation: kineticsTools (RRID:SCR_024049) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://itk.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/jnktsj/DNApi/

Software de novo adapter prediction algorithm for small RNA sequencing data.

Proper citation: DNApi (RRID:SCR_024009) Copy   

•   Source: SciCrunch Registry

http://assemblytics.com/

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   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/microbegps/

Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates.

Proper citation: MicrobeGPS (RRID:SCR_024112) Copy   

•   Source: SciCrunch Registry

http://gmod.org/wiki/Chado

Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.

Proper citation: Chado (RRID:SCR_024073) Copy   

•   Source: SciCrunch Registry

https://plast.inria.fr/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://spaced.gobics.de/

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   

•   Source: SciCrunch Registry

https://www.sofa-framework.org/

Open source software framework targeting at real-time simulation, with emphasis on medical simulation.

Proper citation: sofa-apps (RRID:SCR_024346) Copy   

•   Source: SciCrunch Registry