Jit
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MGcV: the microbial genomic context viewer for comparative genome analysis
By Jit 2491 days agohttp://mgcv.cmbi.ru.nl/ - MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV: Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by selecting the type of identifier...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2385 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...
Download blasr 1.3 version
By Jit 2354 days agoDOWNLOAD LINK: https://github.com/BioInf-Wuerzburg/proovread/raw/master/util/blasr-1.3.1/blasr I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error: fail to open file './temporarySam' [bwa_aln_core] write to the...GFinisher: a new strategy to refine and finish bacterial genome assemblies
By Jit 2313 days agogfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...MITOS: improved de novo metazoan mitochondrial genome annotation
By Jit 2221 days agomitos.bioinf.uni-leipzig.de - Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene...ASCIIGenome: genome browser based on command line interface and designed for running from console...
By Neel 2207 days ago Comments (2)github.com - ASCIIGenome is a genome browser based on command line interface and designed for running from console terminals. Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data...genoPlotR - plot gene and genome maps project!
By Abhimanyu Singh 2174 days agogenoplotr.r-forge.r-project.org - genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear...GenomeView: genome browser and annotation editor
By Rahul Nayak 2153 days agosourceforge.net - GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.This project has...The Rogers Lab
The Rogers lab studies evolution of genome structure. We explore the ways that complex mutations like duplications, deletions, rearrangements, and retrogenes can create new genetic material. We study how these new mutations are important for...ALF--a simulation framework for genome evolution.
By Jit 1860 days agohttp://alfsim.org/#index - Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article: Daniel A Dalquen,...
