List of gene ontology software and tools
...ms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds. http://revig...3709 days ago
String graph based genome assembly software and tools !
...curves in the plane; each curve is called a "string". String graphs were first proposed by E. W....ii) Simpson-Durbin algorithm is that it does not rely on de Bruijn graphs, and instead employs a differ...2328 days ago
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Bioinformatics algorithms tutorials
Useful bioinformatics tutorial, such as De Bruijn Graphs for NGS AssemblyAlgorithms for PacBio ReadsSoftware and Hardware Concepts for BioinformaticsFinding us in Homolog.us (Search...3602 days ago
A guide for complete R beginners :- Getting data into R
...spaces in a columns with ‘NA’ . The last two examples will still work with our file and give the same result as with only headers=T Graphs to get an idea of what R is...3357 days ago
Genome Assembly Tools and Software - PART2 !!
...sp;is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both sha...l variants assembling based on maximum-bandwidth paths in weighted read graphs and frequency estimation via...2685 days ago
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3945 days ago
Release Notes for Genome Workbench 2.10.5
...eatures in latest release New ProSplign tool integrated with Genome Workbench (Tutorial, Video) New export function for BAM/cSRA coverage graphs (Tutorial) New export functi...2914 days ago
Pack a perl program with their dependencies on Ubuntu !
...hub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with...1510 days ago
MGRA: Breakpoint graphs and ancestral genome reconstructions
MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes. It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the in...Tags: MGRA, Breakpoint, graphs, ancestral, genome, reconstructions
2475 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is ...Tags: RGFA, powerful, convenient, handling, assembly, graphs, GFA
1566 days ago
Comment on "Sibelia: A comparative genomics tool"
...son Tool" (poster), WABI 2012 http://bioinf.spbau.ru/sites/default/files/SyntenyFinder.pdf 2. Max A. Alekseyev and Pavel A. Pevzner. "Breakpoint graphs and ancestral genome reconst...1284 days ago
2136 days ago