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https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw
Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.
Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy
https://sourceforge.net/projects/tab2mage/
Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.
Proper citation: Tab2MAGE (RRID:SCR_024101) Copy
https://metacpan.org/dist/Bio-Tools-Phylo-PAML
Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.
Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy
http://colibread.inria.fr/software/mapsembler2/
Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.
Proper citation: Mapsembler2 (RRID:SCR_024102) Copy
https://github.com/gerddie/maxflow
Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.
Proper citation: MAXFLOW (RRID:SCR_024103) Copy
https://metacpan.org/dist/Bio-Graphics
Software package to generate GD images of Bio::Seq objects.
Proper citation: Bio-Graphics (RRID:SCR_024061) Copy
https://github.com/genouest/biomaj-cli
Software package to use BioMAJ providing biomaj-cli.
Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy
Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.
Proper citation: BCALM 2 (RRID:SCR_023975) Copy
https://github.com/gpertea/gclib
Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.
Proper citation: GCLib (RRID:SCR_024028) Copy
Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.
Proper citation: CAT and BAT (RRID:SCR_023988) Copy
https://github.com/RoelofBerg/limereg
Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.
Proper citation: limereg (RRID:SCR_024097) Copy
https://neobio.sourceforge.net/
Software library of sequence alignment algorithms implemented in Java.
Proper citation: NeoBio (RRID:SCR_024131) Copy
https://github.com/xdf-modules/libxdf
Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.
Proper citation: Libxdf (RRID:SCR_024096) Copy
https://github.com/mroosmalen/nanosv
Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.
Proper citation: NanoSV (RRID:SCR_024127) Copy
https://github.com/WorkflowConversion/CTDConverter
Software Python scripts to convert CTD files into other formats such as Galaxy, CWL.
Proper citation: CTDConverter (RRID:SCR_024007) Copy
https://github.com/wdecoster/NanoPlot
Software package as plotting tool for long read sequencing data and alignments.
Proper citation: NanoPlot (RRID:SCR_024128) Copy
https://freeimage.sourceforge.io/
Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.
Proper citation: FreeImage (RRID:SCR_024022) Copy
https://github.com/bioinfo-ut/GenomeTester4
Software toolkit for performing set operations - union, intersection and complement on k-mer lists.
Proper citation: GenomeTester4 (RRID:SCR_024026) Copy
GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.
Proper citation: GDCM (RRID:SCR_024027) Copy
https://github.com/nextstrain/augur
Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines.
Proper citation: Augur (RRID:SCR_023964) Copy
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