<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44641?offset=40 https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments Mon, 22 Sep 2025 23:51:02 -0500 https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments <![CDATA[Termal: a fast and interactive terminal-based viewer for multiple sequence alignments]]> termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

]]> 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)
]]> Jit https://bioinformaticsonline.com/bookmarks/view/27432/gkno Fri, 20 May 2016 18:56:37 -0500 https://bioinformaticsonline.com/bookmarks/view/27432/gkno <![CDATA[GKNO]]> gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.

http://gkno.me/how-to/install.html

http://gkno.me/software.html

Address of the bookmark: http://gkno.me/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines Wed, 15 Jun 2016 17:18:36 -0500 https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines <![CDATA[LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines]]> LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.

Publication:

  • L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.

Download:

Address of the bookmark: https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/30680/easybuild Fri, 27 Jan 2017 16:00:43 -0600 https://bioinformaticsonline.com/bookmarks/view/30680/easybuild <![CDATA[EasyBuild]]> EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32948/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology Tue, 23 May 2017 05:28:56 -0500 https://bioinformaticsonline.com/bookmarks/view/32948/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology <![CDATA[SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology]]> SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/35896/phylographer-graph-visualization-tool Wed, 07 Mar 2018 18:11:25 -0600 https://bioinformaticsonline.com/bookmarks/view/35896/phylographer-graph-visualization-tool <![CDATA[PhyloGrapher - Graph Visualization Tool]]> PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements. 

https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42204/g-nest-the-gene-neighborhood-scoring-tool Fri, 25 Sep 2020 20:09:18 -0500 https://bioinformaticsonline.com/bookmarks/view/42204/g-nest-the-gene-neighborhood-scoring-tool <![CDATA[G-NEST: The Gene NEighborhood Scoring Tool]]> The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin. Example data files are in the separate repository.

Address of the bookmark: https://github.com/dglemay/G-NEST

]]> Neel https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome Thu, 08 Aug 2024 23:31:18 -0500 https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome <![CDATA[Tools to access the quality of your assembled genome !]]>
  • FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation
  • GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation
  • ASSEMBLATHON STATS: Assembly statistics
  • GENOMETOOLS GT STAT: Annotation statistics
  • NCBI FCS ADAPTOR: Adaptor contamination pass/fail
  • NCBI FCS GX: Foreign organism contamination pass/fail
  • BUSCO: Gene-space completeness estimation
  • TIDK: Telomere repeat identification
  • LAI: Continuity of repetitive sequences
  • KRAKEN2: Taxonomy classification
  • HIC CONTACT MAP: Alignment and visualisation of HiC data
  • MUMMER → CIRCOS + DOTPLOT & MINIMAP2 → PLOTSR: Synteny analysis
  • MERQURY: K-mer completeness, consensus quality and phasing assessment
    • ]]>     LEGE