BOL: Related items

FigTree

Rahul Nayak — Wed, 19 Jul 2017 08:06:45 -0500

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.

Address of the bookmark: http://tree.bio.ed.ac.uk/software/figtree/

TMRCA Calculator

BioStar — Wed, 03 Feb 2021 05:07:30 -0600

This program calculates the probability that two people have a certain number of generations between them, based on the standard infinite alleles formula of Walsh. It calculates both the probability of being at an exact number of generations back to the Most Recent Common Ancestor (MRCA) of a certain pair of people and the cumulative probability that the actual number of generations is less than a certain value. Note that the convention using generations is changed from an earlier version of this calculator which used "transmission events". It can list both result types in a table or graph. In either case the horizontal axis stops at the point where the cumulative probability reaches 95% or 10 generations, whichever is longer, or an absolute max of 50,000. Beyond 90% the calculation becomes inaccurate.

https://clandonaldusa.org/index.php/tmrca-calculator

Address of the bookmark: https://clandonaldusa.org/index.php/tmrca-calculator

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction

Abhi — Mon, 08 Apr 2024 06:19:52 -0500

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 coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

BLAST Ring Image Generator (BRIG)

Anjana — Fri, 30 Sep 2016 09:18:50 -0500

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at: http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page: http://sourceforge.net/tracker/?group_id=328245.

Features:

Images show similarity between a central reference sequence and other sequences as concentric rings.
BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

Address of the bookmark: http://brig.sourceforge.net/

CGView.js is a Circular Genome Viewing tool

LEGE — Wed, 27 Mar 2024 11:16:24 -0500

CGView.js is a Circular Genome Viewing tool for visualizing and interacting with small genomes. This software is an adaptation of the Java program CGView.

CGView.js is the genome viewer of Proksee, an expert system for genome assembly, annotation and visualization.

Features

Circular and linear views of genomes
Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs
Smooth zooming down to the sequence level
Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)
Save high resolution PNG maps up to 8000x8000px
Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

gggenes: a ggplot2 extension for drawing gene arrow maps.

BioStar — Tue, 02 Jun 2020 11:43:34 -0500

Install the stable version of gggenes from CRAN:

install.packages("gggenes")

If you want the development version, install it from GitHub:

devtools::install_github("wilkox/gggenes")

More at https://github.com/wilkox/gggenes

Address of the bookmark: http://wilkox.org/gggenes

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

Kevler: Reference-free variant discovery in large eukaryotic genomes

Jit — Tue, 28 Jan 2020 03:21:53 -0600

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model.

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

Genetic-mapper: SVG Genetic Map Drawer

Jit — Sun, 18 Jun 2017 14:11:10 -0500

Genetic-mapper is a perl script able to draw publication-ready vectorial genetic maps.

Perl script for creating a publication-ready vectorial genetic/linkage map in Scalable Vector Graphics (SVG) format. The resulting file can either be submitted for publication and edited with any vectorial drawing software like Inkscape and Abobe Illustrator(R).

The input file must be a text file with at least the marker name (ID), linkage group (LG) and the position (POS) separeted by tabulations. Additionally a logarithm of odds (LOD score) can be provided. Any extra parameter will be ignored.

map.tsv

IDLGPOSLOD
13519  12     0       0.250840894
2718   12     1.0     0.250840893
11040  12     1.6     0.252843341
...

https://github.com/pseudogene/genetic-mapper

Address of the bookmark: https://github.com/pseudogene/genetic-mapper

alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Jit — Mon, 12 Mar 2018 09:24:40 -0500

Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr

http://www.mdpi.com/2073-4425/8/10/248

Address of the bookmark: http://alienness.sophia.inra.fr/cgi/index.cgi