BOL: Related items

A web-based tool for sequence alignment statistics and innovative visualization

BioStar — Thu, 04 Apr 2024 01:44:50 -0500

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 results. Whencompared to currently available tools, AlignStatPlot provides a robust ability to handle andvisualise diversity data, while the online version will save time and encourage researchersto focus on explaining their findings. It is a simple tool that can be used in conjunction withpopulation genetics software (PDF) AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data.

Address of the bookmark: https://bioinformatics.um6p.ma/AlignStatPlot/

Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences

LEGE — Sun, 31 Aug 2025 06:30:16 -0500

Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.

Address of the bookmark: https://github.com/MGXlab/Jaeger

RepeatModeler2: automated genomic discovery of transposable element families

Neel — Mon, 02 Dec 2019 06:52:29 -0600

RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, https://github.com/Dfam-consortium/TETools).

Address of the bookmark: https://github.com/Dfam-consortium/TETools

ALPHA: A Toolkit for Automated Local Phylogenomic Analyses

Jit — Wed, 21 Mar 2018 18:12:06 -0500

Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It has four distinct modes that are useful for different types of phylogenetic analysis: RAxML, File Converter, MS Comparison, and D-statistic.

Address of the bookmark: https://github.com/chilleo/ALPHA

alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.

Jit — Sun, 02 Feb 2020 13:51:31 -0600

identify potential contaminants or horizontally transferred genes in transcriptomes.

algorithm is based on alogorithm described in the following: Gladyshev, Eugene A., Matthew Meselson, and Irina R. Arkhipova. "Massive horizontal gene transfer in bdelloid rotifers." science 320.5880 (2008): 1210-1213.

alien_index

Address of the bookmark: https://github.com/josephryan/alien_index

DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes

Rahul Nayak — Tue, 30 Mar 2021 11:47:28 -0500

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology.

DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Address of the bookmark: http://www.essentialgene.org/

Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes

LEGE — Wed, 21 Feb 2024 06:13:08 -0600

Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. Our goal was to make it straightforward to work from a combination of input sources including annotated contigs in Genbank format and FASTA files containing CDSs. It uses several state of the art inference methods for orthology inference, either based on HMM profiles or de novo inference of orthogroups. Through the use of OrthoSNAP, many additional ortholog alignments can be generated from multi-copy gene families. For phylogenetic inference, users can choose a supermatrix approach and/or gene tree inference followed by supertree reconstruction. Users can specify a range of alignment filtering settings to retain high-quality alignments for phylogenetic inference. The workflow produces a detailed report that, in addition to the phylogenetic results, includes a range of diagnostics to verify the quality of the results.

Address of the bookmark: https://github.com/rbturnbull/orthoflow

Fourth Branch of Life

Jitendra Narayan — Mon, 09 Sep 2013 21:48:37 -0500

Scientist have found the biggest viruses known, pandoraviruses which opened up entirely /completely... new questions questions and raise objections to in science. It even suggesting a fourth domain of life.

The new visrus are about one micron—a thousandth of a millimeter—in length, the newfound genus Pandoravirus dwarfs other viruses, which range in size from about 50 nanometers up to 100 nanometers. A genus is a taxonomic ranking between species and family.

Find more at @ http://www.nature.com/scitable/blog/viruses101/newly_found_pandoraviruses_hint_at

http://news.nationalgeographic.co.uk/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/

clusterProfiler

Jit — Thu, 16 Jun 2016 18:57:03 -0500

statistical analysis and visulization of functional profiles for genes and gene clusters

Bioconductor version: Release (3.3)

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Author: Guangchuang Yu with contributions from Li-Gen Wang and Giovanni Dall'Olio.

Maintainer: Guangchuang Yu

Citation (from within R, enter citation("clusterProfiler")):

Yu G, Wang L, Han Y and He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287.
Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")

https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Shruti Paniwala — Fri, 03 Jan 2020 13:28:19 -0600

DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life.

Address of the bookmark: https://github.com/YoannAnselmetti/DeCoSTAR_pipeline