<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/32855?offset=30 https://bioinformaticsonline.com/bookmarks/view/34543/acana-an-accurate-and-consistent-alignment-tool-for-dna-sequences Wed, 06 Dec 2017 09:45:29 -0600 https://bioinformaticsonline.com/bookmarks/view/34543/acana-an-accurate-and-consistent-alignment-tool-for-dna-sequences <![CDATA[ACANA: An accurate and consistent alignment tool for DNA sequences]]> ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.

Address of the bookmark: https://www.niehs.nih.gov/research/resources/software/biostatistics/acana/index.cfm

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39837/cactus-a-reference-free-whole-genome-multiple-alignment-program Mon, 12 Aug 2019 07:52:33 -0500 https://bioinformaticsonline.com/bookmarks/view/39837/cactus-a-reference-free-whole-genome-multiple-alignment-program <![CDATA[Cactus: a reference-free whole-genome multiple alignment program]]> Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111

Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should expect Cactus to use approximately 120 CPU-days of compute per genome, with about 120 GB of RAM used at peak. The requirements scale roughly quadratically, so aligning two 1-megabase bacterial genomes takes only 1.5 CPU-hours and 14 GB RAM. 

Address of the bookmark: https://github.com/ComparativeGenomicsToolkit/cactus

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization Thu, 04 Apr 2024 01:44:50 -0500 https://bioinformaticsonline.com/bookmarks/view/44508/a-web-based-tool-for-sequence-alignment-statistics-and-innovative-visualization <![CDATA[A web-based tool for sequence alignment statistics and innovative visualization]]> AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection Wed, 08 May 2024 07:02:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection <![CDATA[Alvis: a tool for contig and read ALignment VISualisation and chimera detection]]> Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/37796/grsr-a-tool-for-deriving-genome-rearrangement-scenarios-from-multiple-unichromosomal-genome-sequences Fri, 28 Sep 2018 09:35:10 -0500 https://bioinformaticsonline.com/bookmarks/view/37796/grsr-a-tool-for-deriving-genome-rearrangement-scenarios-from-multiple-unichromosomal-genome-sequences <![CDATA[GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences]]> GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

  • Step 1. Run mugsy to get multiple sequence alignment results.
  • Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
  • Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38041/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies Tue, 30 Oct 2018 10:49:13 -0500 https://bioinformaticsonline.com/bookmarks/view/38041/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies <![CDATA[Synima: a Synteny imaging tool for annotated genome assemblies]]> Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/41125/chromonomer-a-tool-set-for-repairing-and-enhancing-assembled-genomes-through-integration-of-genetic-maps-and-conserved-synteny Mon, 17 Feb 2020 05:38:46 -0600 https://bioinformaticsonline.com/bookmarks/view/41125/chromonomer-a-tool-set-for-repairing-and-enhancing-assembled-genomes-through-integration-of-genetic-maps-and-conserved-synteny <![CDATA[Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny]]> 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 assembled according to the genetic map, and split those scaffolds.

Address of the bookmark: http://catchenlab.life.illinois.edu/chromonomer/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44525/synorth-exploring-the-evolution-of-synteny-and-long-range-regulatory-interactions-in-vertebrate-genomes Mon, 06 May 2024 06:21:10 -0500 https://bioinformaticsonline.com/bookmarks/view/44525/synorth-exploring-the-evolution-of-synteny-and-long-range-regulatory-interactions-in-vertebrate-genomes <![CDATA[Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes]]> Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745767/

Address of the bookmark: http://synorth.genereg.net/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/27110/easyfig Fri, 29 Apr 2016 05:49:39 -0500 https://bioinformaticsonline.com/bookmarks/view/27110/easyfig <![CDATA[Easyfig]]> Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig.  Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/

]]> Poonam Mahapatra https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 Thu, 12 May 2016 13:49:41 -0500 https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105 <![CDATA[Release Notes for Genome Workbench 2.10.5]]> New Features in latest release

  • New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
  • New export function for BAM/cSRA coverage graphs (Tutorial)
  • New export function for alignments GFF3 format ((Tutorial))
  • Tree View: implemented new export mode based on selections (tutorial coming)
  • Tree View: added support for distance based circular trees
  • Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
  • Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)
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