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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
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
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
https://github.com/PyWavelets/pywt
Software Python package for wavelet analysis.
Proper citation: PyWavelets (RRID:SCR_024421) 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
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
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://sciex.com/products/software/proteinpilot-software
Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.
Proper citation: ProteinPilot (RRID:SCR_024414) Copy
https://github.com/paulgeeleher/pRRophetic
Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,
Proper citation: pRRophetic (RRID:SCR_024417) 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://qtlreaper.sourceforge.net/
Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL.
Proper citation: qtlreaper (RRID:SCR_024199) 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
https://sparta.readthedocs.io/en/latest/
Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.
Proper citation: sparta (RRID:SCR_024349) 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
https://github.com/bartongroup/yanosim
Software tool as read simulator for nanopore DRS datasets.
Proper citation: Yanosim (RRID:SCR_024363) Copy
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