BOL: Related items

Chickenosaurus on the way !!

Jit — Tue, 12 Nov 2013 21:40:34 -0600

Hmmm .. Now they know the facts, be careful they might come back as Chickenosaurus. :)

destruct

Jitendra Prajapati — Mon, 29 Feb 2016 17:34:59 -0600

Destruct is a tool for joint prediction of rearrangement breakpoints from single or multiple tumour samples.

More at https://bitbucket.org/dranew/destruct

Address of the bookmark: https://bitbucket.org/dranew/destruct

Synteny and Rearrangement Identifier (SyRI)

Jit — Tue, 05 May 2020 10:37:10 -0500

SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions.

Address of the bookmark: https://schneebergerlab.github.io/syri/

Reference-free prediction of rearrangement breakpoint reads

Neel — Thu, 08 Mar 2018 05:05:25 -0600

lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100×, it finds ∼88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome.

https://github.com/ewijaya/slidesort-bpr

Address of the bookmark: https://code.google.com/archive/p/slidesort-bpr/

Lifemap

Jit — Mon, 10 Apr 2017 05:42:37 -0500

Lifemap is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in Lifemap is similar to the one used in cartography with tools like Google Maps© or Open Street Maps: exploring is done by zooming and panning.

The current tree contains ALL species present in NCBI taxonomy as of October 18th, 2016: 1,135,169 species including 10,545 Archaea, 418,777 Bacteria and 705,847 Eukaryotes. The Lifemap tree is updated every two weeks.

All the nodes in the tree are clickable. This displays various information and options:

The species name (and the associated common name if there is one)
The rank (kingdom, family, class, species...)
Ability to go to the corresponding node/species on NCBI web site (displayed in a new window)
Possibility to download the corresponding subtree in newick extended format
Possibilty to get the whole lineage from the current node/tip to the root of the tree.

Address of the bookmark: http://lifemap-ncbi.univ-lyon1.fr/

Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees

Rahul Nayak — Wed, 27 Nov 2019 05:32:33 -0600

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

ETE, version: 3.1.1
BioPython, version: 1.73
taxadb, version: 0.10.1
TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

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

Radka Reifová Lab

Mon, 15 Feb 2016 06:00:48 -0600

We are generally interested in the mechanisms of species origin from a molecular and ecological perspective. Particularly, we are interested in the role of sex chromosomes in speciation. Most of our research is done on birds and mammals. Currently, we focus our research on two hybridizing song birds, the Common nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia). Combining population genomic and ecological approaches we try to elucidate the genetic architecture of reproductive isolation and understand the role of interspecific competition and song convergence in the evolution of reproductive isolation between the species.

More at http://web.natur.cuni.cz/~radkas/index.php?page=research