<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36720?offset=20 https://bioinformaticsonline.com/bookmarks/view/43806/genomicus-genome-browser-that-enables-users-to-navigate-in-genomes-in-several-dimensions Mon, 28 Feb 2022 23:27:37 -0600 https://bioinformaticsonline.com/bookmarks/view/43806/genomicus-genome-browser-that-enables-users-to-navigate-in-genomes-in-several-dimensions <![CDATA[Genomicus: genome browser that enables users to navigate in genomes in several dimensions]]> Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.

All the data on extant species displayed in this browser are from Ensembl.


Summary statistics of Genomicus version 105.01: (view species tree in pdf or newick)

Number of extant species 200
Number of extant genes 4303993
 
Number of ancestral species 196
Number of ancestral genes 4624213
Number of ancestral synteny blocks 83342

Address of the bookmark: https://www.genomicus.bio.ens.psl.eu/genomicus-105.01/cgi-bin/search.pl

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications Thu, 23 Jul 2020 05:49:45 -0500 https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications <![CDATA[wgd—simple command line tools for the analysis of ancient whole-genome duplications]]> wgd is a easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

https://academic.oup.com/bioinformatics/article/35/12/2153/5162749

Address of the bookmark: https://github.com/arzwa/wgd

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions Tue, 11 Dec 2018 08:43:51 -0600 https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions <![CDATA[regioneR: an R package for the management and comparison of genomic regions]]> Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's possible to study the association of a set of regions with other sets of regions, functions defined over the genome or essentially any user defined function.

http://gattaca.imppc.org/regioner/

Address of the bookmark: http://gattaca.imppc.org/regioner/

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