Results for "Synteny"
Tags
xmatchview: smith-waterman alignment visualization
xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run...Tags: xmatchview, smith-waterman, alignment, visualization, synteny
2316 days ago
Apollo: a sequence annotation editor
The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet thi...Tags: Apollo, sequence, annotation, editor, synteny
1710 days ago
- Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assemb...
Tags: Chromonomer, tool, repairing, enhancing, assembled, genomes, integration, genetic, maps, conserved, synteny
1536 days ago
JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wikiTags: JCVI, Python, utility, libraries, genome, assembly, annotation, comparative, genomics, synteny, plots
1507 days ago
flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and relaxed handling of mismatches and ambiguous residue...Tags: Highly, customizable, ambiguity, aware, dotplots, visual, sequence, analyses, synteny
1469 days ago
Sibelia: A comparative genomics tool
Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for mu...Tags: Sibelia, comparative, genomics, tool, synteny
1349 days ago
chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes
To create a fresh environment for chromatiblock to run in do: conda create --name chromatiblock conda activate chromatiblock conda install chromatiblock --channel conda-forge --channel bioconda Then in future to run chromatiblock you can reactivate this environemtn using conda activate...Tags: chromatiblock, Scalable, whole-genome, visualisation, structural, changes, prokaryotes, synteny
1347 days ago
- Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Tags: MCscan, pipeline, synteny, plant, annotation, comparative genomics, jcvi
1089 days ago
- Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
Tags: Syri, compares, alignments, chromosome-level, assemblies, synteny, structural, rearrangements
701 days ago
JBrowse 2: a modular genome browser with views of synteny and structural variation
igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests) jb2-web - stock instance of jbrowse-web v1.7.5 jb1 - stock instance...Tags: JBrowse, modular, genome, browser, views, synteny, structural, variation
372 days ago
- « Previous
- 1
- 2
- 3
- Next »
