WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify...1006 days ago
RNA-seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-seq differential expression workflow usi...antified to the reference transcripts, and prepare gene-level count datasets for down...relationship between samples, perform differential gene expres...990 days ago
Introduction to phylogenies in R
R phylogenetics is built on the contributed packages for phylogenetics in R, and there are many such packages. Let's begin today by installing a few critical packages, such as ape, phang...987 days ago
922 days ago
GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes
A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one or several taxa...database and searched for the respective gene. Alternatively, custom genome...lized, enabling comparison of synteny and gene conten...911 days ago
898 days ago
GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools&nbs...metools” which consists of several modules. If you are interested in gene predic...875 days ago
AGORA: Algorithm for Gene Order Reconstruction in Ancestors
AGORA stands for “Algorithm for Gene Order Reconstruction in Ancestors” and was...___/ / // | | // | | AGORA is used to generate ancestral genomes for the Genomicus online server for gene order...848 days ago
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...long evolutionary time. Once a query gene has been entered, it is displ...the ancestral species within the phylogenetic range of interest. All th...tant species 200 Number of extant genes 4303...848 days ago
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL lice...769 days ago