Results for "benchmarking and designing tools"
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xmatchview: smith-waterman alignment visualization
xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between...s in fasta format using cross_match and displ...ariety of image formats. xmatchview and xmatchview-conifer are written...x and windows. They serve as visual tools for analyzing cross_match ali...2326 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dud...ogy below is consistent with this paper, and all references to figures and...”. In addition, the pipeline uses tools and methods from Juicer (Duran...2326 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This...bility rate). Simulating reads from random locations in the genome bas...gth, coverage, sequencing error rate, and indel rate. Applying alignment tools to the genome and the reads t...2320 days ago
ECTOOLS: Long Read Correction and other Correction tools
Long Read Correction and other Correction tools This package is a loose collection of scripts. T...correction algorithm takes as input the unitigs from a short read assembly and uses them to correct long read...2318 days ago
LRCstats: Long Read Correction Statistics
LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long...ong read correction algorithms are better than others, and devel...ay alignments between the uncorrected long reads (uLR) and t...2318 days ago
Mobyle: a new full web bioinformatics framework
Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powe...agement features that allow the user to reproduce analyses and to combine tools using a hierarchical typing s...2316 days ago
GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome...It is based on a C library named “libgenometools” which consists of seve...2285 days ago
Circoletto: visualizing sequence similarity with Circos
Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of seque...arity search results. Online version and downl...lable at http://bat.ina.certh.gr/tools/circoletto/ Contact:ndarz@ce...2283 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in compara...es include (i) building gene-based and super...rent size or including duplications, and (iv) providing seamless integ...2273 days ago
Protein Subcellular Localization Prediction
Assigning subcellular localization to a protein is an important step to...g its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools off...tractive complement to time-consuming and laborious experimental methods....2263 days ago
