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Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage.
Proper citation: CodonW (RRID:SCR_023989) Copy
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
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
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
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
https://bitbucket.org/Glouvel/metabit/wiki/Home
Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.
Proper citation: metaBIT (RRID:SCR_024111) Copy
https://mhap.readthedocs.io/en/stable/
Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data.
Proper citation: MHAP (RRID:SCR_024113) Copy
https://github.com/GATB/MindTheGap
Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.
Proper citation: MindTheGap (RRID:SCR_024115) Copy
https://jydu.github.io/maffilter/
Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.
Proper citation: MafFilter (RRID:SCR_024105) Copy
http://maude.cs.illinois.edu/w/index.php/The_Maude_System
Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation.
Proper citation: Maude (RRID:SCR_024108) Copy
https://github.com/Pas-Kapli/mptp
Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.
Proper citation: mPTP (RRID:SCR_024121) Copy
http://ugovaretto.github.io/molekel/
Open source multi platform molecular visualization program.
Proper citation: Molekel (RRID:SCR_024122) Copy
Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
Proper citation: MRtrix3 (RRID:SCR_024123) Copy
Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions.
Proper citation: CTSim (RRID:SCR_024004) Copy
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
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
https://github.com/babinyurii/recan
Software tool as genetic distance plotting for recombination events analysis.
Proper citation: recan (RRID:SCR_024317) Copy
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
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
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
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