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https://bitbucket.org/genomicepidemiology/kmerresistance/src/master/

Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available.

Proper citation: KmerResistance (RRID:SCR_024058) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/PROFisis

Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.

Proper citation: PROFisis (RRID:SCR_024179) Copy   

•   Source: SciCrunch Registry

http://proda.stanford.edu/

Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.

Proper citation: ProDA (RRID:SCR_024171) Copy   

•   Source: SciCrunch Registry

https://ukoethe.github.io/vigra/

Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework.

Proper citation: VIGRA (RRID:SCR_024100) Copy   

•   Source: SciCrunch Registry

https://github.com/biocore/pynast

Software tool for aligning sequences to template alignment.

Proper citation: pynast (RRID:SCR_024189) Copy   

•   Source: SciCrunch Registry

https://www.imsc.res.in/~rsidd/sigma/

Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step.

Proper citation: sigma-align (RRID:SCR_024337) Copy   

•   Source: SciCrunch Registry

https://github.com/ArtRand/signalAlign

Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments,

Proper citation: signalalign (RRID:SCR_024339) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/patristic/

Software Java program for calculating patristic distances and graphically comparing the components of genetic change.

Proper citation: Patristic (RRID:SCR_024154) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-ut/PlasmidSeeker

Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.

Proper citation: PlasmidSeeker (RRID:SCR_024167) Copy   

•   Source: SciCrunch Registry

https://github.com/babinyurii/recan

Software tool as genetic distance plotting for recombination events analysis.

Proper citation: recan (RRID:SCR_024317) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Lighter

Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.

Proper citation: Lighter (RRID:SCR_024095) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-center-pasteur-fr/toppred

Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.

Proper citation: toppred (RRID:SCR_024385) Copy   

•   Source: SciCrunch Registry

http://www.nematodes.org/bioinformatics/trace2dbEST/

Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST.

Proper citation: trace2dbEST (RRID:SCR_024386) Copy   

•   Source: SciCrunch Registry

https://github.com/sina-cb/Tn-seqExplorer

Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.

Proper citation: Tn-seq explorer (RRID:SCR_024387) Copy   

•   Source: SciCrunch Registry

http://saclab.tamu.edu/essentiality/transit/

Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.

Proper citation: TRANSIT (RRID:SCR_024389) Copy   

•   Source: SciCrunch Registry

http://www.tree-puzzle.de

Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.

Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure

Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions.

Proper citation: NORSp (RRID:SCR_024139) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/Metastudent

Software tool to predict gene ontology terms for protein sequences through homology.

Proper citation: Metastudent (RRID:SCR_024110) Copy   

•   Source: SciCrunch Registry

https://github.com/Martinsos/edlib

Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.

Proper citation: Edlib (RRID:SCR_024078) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/Glouvel/metabit/wiki/Home

Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.

Proper citation: metaBIT (RRID:SCR_024111) Copy   

•   Source: SciCrunch Registry