:: DESCRIPTION
DistG counts the length of fasta sequences and make a graphical representation about. There are two king of graphs. The first is the distribution graph, giving an overview of all read fasta files (sequences) so far. The second graph displays a specific file’s counting as a set of rectangles.
::DEVELOPER
Institute of Bioinformatics WWU Muenster
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
veRNAl is an algorithm for identifying fuzzy recurrent subgraphs in RNA 3D networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oliver C, Mallet V, Philippopoulos P, Hamilton WL, Waldispühl J.
VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA.
Bioinformatics. 2021 Nov 15:btab768. doi: 10.1093/bioinformatics/btab768. Epub ahead of print. PMID: 34791045.
:: DESCRIPTION
The EWRA algorithm computes a parsimonious reconstruction of marker adjacencies minimizing the Single-Cut-or-Join (SCJ) distance along a given phylogenetic tree, including the information provided by an assembly graph of ancient DNA (aDNA) data at one internal node of the tree.
::DEVELOPER
Computational Methods for Paleogenomics and Comparative Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Luhmann N, Chauve C, Stoye J, Wittler R.
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov-Dec;15(6):2094-2100. doi: 10.1007/978-3-319-12418-6_17. Epub 2018 Mar 15. PMID: 29993816.
:: DESCRIPTION
GRAFIMO is a command-line tool that extends the traditional Position Weight Matrix (PWM) scanning procedure to VGs.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tognon M, Bonnici V, Garrison E, Giugno R, Pinello L.
GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.
PLoS Comput Biol. 2021 Sep 27;17(9):e1009444. doi: 10.1371/journal.pcbi.1009444. PMID: 34570769; PMCID: PMC8519448.
:: DESCRIPTION
MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.
MCL-edge is a set of ready-made network analysis tools (including MCL) that are single-mindedly focussed at analysis of very large networks, scaling up to millions of nodes and hundreds of millions of edges.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Stijn Van Dongen
Graph clustering via a discrete uncoupling process.
Siam Journal on Matrix Analysis and Applications 30-1, p121-141, 2008.
:: DESCRIPTION
CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2014 Oct 31;15:344. doi: 10.1186/1471-2105-15-344.
CIG-P: Circular Interaction Graph for Proteomics.
Hobbs CK, Leung M, Tsang HH1, Ebhardt HA.
:: DESCRIPTION
PathRacer is a novel standalone tool that aligns profile HMM directly to the assembly graph (performing the codon translation on fly for amino acid pHMMs). The tool provides the set of most probable paths traversed by a HMM through the whole assembly graph, regardless whether the sequence of interested is encoded on the single contig or scattered across the set of edges, therefore significantly improving the recovery of sequences of interest even from fragmented metagenome assemblies.
::DEVELOPER
Center for Algorithmic Biotechnology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
glmgraph is an R package for variable selection and predictive modeling of structured genomic data
::DEVELOPER
Li Chen <li.chen at emory.edu>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
glmgraph: An R Package for Variable Selection and Predictive Modeling of Structured Genomic Data.
Chen L, Liu H, Kocher JA, Li H, Chen J.
Bioinformatics. 2015 Aug 26. pii: btv497.
:: DESCRIPTION
BCALM is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rayan Chikhi, Antoine Limasset and Paul Medvedev,
Compacting de Bruijn graphs from sequencing data quickly and in low memory,
Bioinformatics, 32 (12), i201-i208 2016 Jun 15
:: DESCRIPTION
Bandage (a B: ioinformatics A: pplication for N: avigating De novo A: ssembly G: raphs E: asily) is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers Velvet and SPAdes.
::DEVELOPER
Ryan Wick rrwick@gmail.com
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bandage: interactive visualisation of de novo genome assemblies.
Wick RR, Schultz MB, Zobel J, Holt KE.
Bioinformatics. 2015 Jun 22. pii: btv383
