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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
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
https://gitlab.com/rki_bioinformatics/purple
Software tool for selecting target specific peptide candidates directly from given proteome sequence data.
Proper citation: purple (RRID:SCR_024183) Copy
http://bioinf.spbau.ru/sibelia
Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms.
Proper citation: sibelia (RRID:SCR_024336) Copy
https://sibsim4.sourceforge.net/
Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns.
Proper citation: sibsim4 (RRID:SCR_024338) Copy
http://prodata.swmed.edu/pcma/pcma.php
Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences.
Proper citation: PCMA (RRID:SCR_024156) Copy
https://github.com/brettc/partitionfinder
Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data.
Proper citation: PartitionFinder (RRID:SCR_024157) Copy
https://zhanglab.ccmb.med.umich.edu/TM-align/
Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons.
Proper citation: TM-align (RRID:SCR_024390) Copy
https://github.com/BD2KGenomics/toil
Software pipeline management system, written in Python. Enables reproducible, open source, big biomedical data analyses.
Proper citation: toil (RRID:SCR_024391) Copy
https://gitlab.com/andreas.andrusch/paipline
Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples.
Proper citation: PAIPline (RRID:SCR_024151) Copy
https://sourceforge.net/projects/pipasic/
Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.
Proper citation: pipasic (RRID:SCR_024165) Copy
https://github.com/BU-ISCIII/plasmidID
Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.
Proper citation: PlasmidID (RRID:SCR_024166) Copy
https://bitbucket.org/genomicepidemiology/resfinder
Software tool identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. Used for identification of acquired antimicrobial resistance genes in whole-genome data.
Proper citation: resfinder (RRID:SCR_024314) Copy
https://github.com/reedacartwright/ngila
Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties.
Proper citation: Ngila (RRID:SCR_024133) Copy
https://github.com/medvedevgroup/varmatch
Software tool for variant matching problem.Used for robust matching of small variant datasets using flexible scoring schemes
Proper citation: VarMatch (RRID:SCR_024375) Copy
https://github.com/Nextomics/nextsv
Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.
Proper citation: NextSV (RRID:SCR_024134) Copy
https://github.com/nextflow-io/nextflow
Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.
Proper citation: Nextflow (RRID:SCR_024135) Copy
https://github.com/nawrockie/vadr
Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families.
Proper citation: VADR (RRID:SCR_024377) Copy
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