Virology and Bioi...
Follow
Find tag "phylogeny"
76.3K views | +19 today
Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Cindy
Scoop.it!

Fast genome and metagenome distance estimation using MinHash

Given a massive collection of sequences, it is infeasible to perform pairwise alignment for basic tasks like sequence clustering and search. Our new tool, Mash, uses MinHash locality-sensitive hashing to reduce large sequences to a representative sketch and rapidly estimate pairwise distances between genomes or metagenomes...The resulting 93 MB sketch database includes all RefSeq genomes, effectively delineates known species boundaries, reconstructs approximate phylogenies, and can be searched in seconds using assembled genomes or raw sequencing runs from Illumina, Pacific Biosciences, and Oxford Nanopore. For metagenomics, Mash scales to thousands of samples and can replicate Human Microbiome Project and Global Ocean Survey results in a fraction of the time. Other potential applications include any problem where an approximate, global sequence distance is acceptable, e.g. to triage and cluster sequence data, assign species labels to unknown genomes, quickly identify mis-tracked samples, and search massive genomic databases.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

iPhylo: Viewing phylogenies on the web: Javascript conversion of Newick tree to SVG

iPhylo: Viewing phylogenies on the web: Javascript conversion of Newick tree to SVG | Virology and Bioinformatics from Virology.ca | Scoop.it

very cool!!!

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Reference set for: Multiple Sequence Alignment and Phylogenies

Papers and books on:

Multiple Sequence Alignment and Phylogenies

more...
No comment yet.
Scooped by Ben Hetman
Scoop.it!

Algorithms for Molecular Biology | Full text | Alignment-free phylogeny of whole genomes using underlying subwords

With the progress of modern sequencing technologies a large number of complete genomes are now available. Traditionally the comparison of two related genomes is carried out by sequence alignment.
Ben Hetman's insight:

This is a lot faster way of producing phylogenies than trying to align everything, and may be more accurate when trying to compare recombinogenic sequences. 

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Bacterial phylogenetic tree construction based on genomic translation stop signals

The efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated.
more...
No comment yet.
Scooped by Ben Hetman
Scoop.it!

Phylogeny: Rewriting evolution

Phylogeny: Rewriting evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree.
more...
No comment yet.