Seeing Theory was created by Daniel Kunin while an undergraduate at Brown University. The goal of this website is to make statistics more accessible through interactive visualizations (designed using Mike Bostock’s JavaScript library D3.js).
Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!
Bactopia can be split into two main...
The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC’s biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO...
(perlENV) [raj@hn1 bin]$ ./alienomics_v0.3.2 Can't load '/tmp/par-6a6e61726179616e/cache-b3e30287a6ce7f2b069c63e57901fcbf1d6597d7/5b8c5ac2.so' for module POSIX: /lib64/libm.so.6: version `GLIBC_2.23' not found (required by...
ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate...
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...
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...
Bioinformatics tools play a crucial role in studying viruses, enabling researchers to analyze their genetic makeup, structure, function, and evolution. Here are some commonly used bioinformatics tools for virus...
MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard...
P-value is often discussed when dealing with science. Especially in scientific journals, you will surely find mentions of the p-value. But what is it, really? Well, if I were to explain it in very simple and concise terms, I would say:“Imagine...
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...
