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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://github.com/aschafu/PSSH2
Software tools for creating the sequence-to-structure alignment database PSSH2.
Proper citation: pssh2 (RRID:SCR_024181) Copy
https://pyepl.sourceforge.net/
Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses.
Proper citation: pyepl (RRID:SCR_024182) Copy
https://github.com/PacificBiosciences/pbcopper
Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.
Proper citation: pbcopper (RRID:SCR_024152) Copy
https://harvest.readthedocs.io/en/latest/content/parsnp.html
Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
Proper citation: Parsnp (RRID:SCR_024153) Copy
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.
Proper citation: PDB2PQR (RRID:SCR_024155) Copy
https://github.com/sib-swiss/pftools3
Software suite of tools to build and search generalized profiles.
Proper citation: PfTools (RRID:SCR_024158) Copy
https://jydu.github.io/physamp/
Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.
Proper citation: PhySamp (RRID:SCR_024159) Copy
https://sourceforge.net/projects/parsinsert/
Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.
Proper citation: ParsInsert (RRID:SCR_024163) Copy
https://github.com/bxlab/bx-python
Software Python library and associated set of scripts for rapid implementation of genome scale analyses.
Proper citation: python-bx (RRID:SCR_024202) 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
http://murasaki.dna.bio.keio.ac.jp/wiki/
Software language-theory based homology detection tool across multiple large genomes.
Proper citation: Murasaki (RRID:SCR_024132) Copy
https://www.ncbi.nlm.nih.gov/books/NBK179288/
Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.
Proper citation: Entrez Direct (RRID:SCR_024136) Copy
https://doua.prabi.fr/software/njplot
Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Proper citation: NJplot (RRID:SCR_024137) 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/wdecoster/NanoPlot
Software package as plotting tool for long read sequencing data and alignments.
Proper citation: NanoPlot (RRID:SCR_024128) Copy
https://pypi.org/project/OBITools/
Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.
Proper citation: OBITools (RRID:SCR_024141) Copy
https://www.orthanc-server.com/
Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.
Proper citation: Orthanc (RRID:SCR_024145) Copy
https://www.rostlab.org/owiki/index.php/Norsnet
Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data.
Proper citation: NORSnet (RRID:SCR_024146) Copy
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