BOL: Related items

Interactive Bioinformatics Resources !

Jit — Thu, 12 Aug 2021 00:09:00 -0500

Learn how to use bioinformatics tools right from your browser.
Everything runs in a sandbox, so you can experiment all you want.

More at sandbox.bio

Address of the bookmark: http://sandbox.bio

dotPlotly: Generate an interactive dot plot from mummer or minimap alignments

Rahul Nayak — Thu, 21 Feb 2019 10:22:17 -0600

Create an interactive dot plot from mummer output OR PAF format

R script that makes a plotly interactive and/or static (png/pdf) dot plot.

Shiny app available for testing

Address of the bookmark: https://github.com/tpoorten/dotPlotly

shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams

Jit — Sat, 29 Feb 2020 00:39:50 -0600

shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package.

To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to the Single-genome plot menu.

To cretae two-genome plot for comparison of data across two genomes, go to the Two-genome plot menu.

For the detail format of input data, check the Input data format submenu of the Help menu.

shinyChromosome is deployed at http://150.109.59.144:3838/shinyChromosome/, http://shinyChromosome.ncpgr.cn, and https://yimingyu.shinyapps.io/shinyChromosome for online use. The source code and manual of shinyChromosome are freely available at https://github.com/venyao/shinyChromosome.

https://yimingyu.shinyapps.io/shinychromosome/

https://www.sciencedirect.com/science/article/pii/S1672022919301883

Address of the bookmark: https://yimingyu.shinyapps.io/shinychromosome/

slacTree: SVG Large Annotated Circular Tree drawing

Jit — Mon, 03 Jul 2017 08:02:56 -0500

A simple, extensible, Perl script for producing figures of large phylogenetic trees.

While there are many other tree drawing programs, slacTree was originally written in 2009 to fill a need for producing publication quality figures of circular trees with more than 1000 taxa with custom annotations
Because it is a single Perl script with very few dependencies, it is easy to run, and easy to further customize
SVG is used because it is a scalable format allowing for very small representations of entire trees or highly magnified regions with unlimited resolution
Circular and radial trees are more compact than linear representations

Address of the bookmark: https://github.com/mccrowjp/slacTree

Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical programming environment.

Jit — Tue, 21 Jan 2020 04:22:49 -0600

Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the DeltaRho environment.

For those familiar with Trellis Display, faceting in ggplot, or the notion of small multiples, Trelliscope provides a scalable way to break a set of data into pieces, apply a plot method to each piece, and then arrange those plots in a grid and interactively sort, filter, and query panels of the display based on metrics of interest. With Trelliscope, we are able to create multipanel displays on data with a very large number of subsets and view them in an interactive and meaningful way.

Address of the bookmark: http://deltarho.org/docs-trelliscope/#introduction

Katju Lab

Fri, 26 Feb 2016 03:25:32 -0600

TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

SISRS: Site Identification from Short Read Sequences

Abhimanyu Singh — Wed, 28 Nov 2018 08:56:03 -0600

Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.

Address of the bookmark: https://github.com/rachelss/SISRS

KAST

Neel — Wed, 23 Feb 2022 08:28:36 -0600

Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

Address of the bookmark: https://github.com/martinjvickers/KAST

KAST: Perform Alignment-free k-tuple frequency comparisons from sequences

Jit — Thu, 20 Sep 2018 08:56:35 -0500

Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

Address of the bookmark: https://github.com/martinjvickers/KAST

SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences

Jit — Wed, 12 Dec 2018 09:22:41 -0600

The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.

SiLiX adopts a graph-theoretical framework to interpret similarity pairs as edges of a network. A very efficient algorithm, based on the Disjoint Sets Data Structure, allows the computation of sequence families with low time and space requirements.

A parallel version of SiLiX, based on MPI, is also available in this package and has been proved to be scalable, so that its allows the study of very large datasets.

SiLiX is already included in the analysis pipeline for HOGENOM.

Address of the bookmark: http://lbbe.univ-lyon1.fr/SiLiX?lang=fr