Featured Research

from universities, journals, and other organizations

New software automates and improves phylogenomics from next-generation sequencing data

Date:
March 6, 2014
Source:
Molecular Biology and Evolution (Oxford University Press)
Summary:
To reconstruct phylogenetic trees from next-generation sequencing data using traditional methods requires a time-consuming combination of bioinformatic procedures including genome assembly, gene prediction, orthology identification and multiple alignment. Now a new online tool called REALPHY reconstructs evolutionary trees from data generated by next-generation sequencing data in a way that avoids these errors and biases.

To reconstruct phylogenetic trees from next-generation sequencing data using traditional methods requires a time-consuming combination of bioinformatic procedures including genome assembly, gene prediction, orthology identification and multiple alignment. As a consequence, more recently, scientists have relied on a simpler method where short sequence reads from each species are aligned directly to the genome sequence of a single reference sequence.

The authors, Bertels, et. al., in the advanced online edition of Molecular Biology and Evolution, not only show that this simpler method can lead to significant errors and biases in phylogeny reconstruction, but have also developed a new online tool called REALPHY (reference sequence alignment based phylogeny builder) that automatically reconstructs evolutionary trees from data generated by next-generation sequencing data in a way that avoids these errors and biases. Applying this new method to several collections of bacterial genomes, the authors show that the method is at least as accurate, and often more accurate, than traditional methods.

"We believe REALPHY will make it easy for any researcher to obtain accurate phylogenies from next-generation sequencing data," said corresponding author Frederic Bertels of the University of Basel, Switzerland.

The software is simple enough for biologists without much bioinformatics expertise to use. REALPHY is available through a webserver, allowing for the fast and automated generation of multiple sequence alignments from a variety of genome sequence data formats (e.g., Illumina sequences, draft genomes, fully sequenced genomes), and the automated reconstruction of phylogenies from these alignments.


Story Source:

The above story is based on materials provided by Molecular Biology and Evolution (Oxford University Press). Note: Materials may be edited for content and length.


Journal Reference:

  1. F. Bertels, O. K. Silander, M. Pachkov, P. B. Rainey, E. van Nimwegen. Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution, 2014; DOI: 10.1093/molbev/msu088

Cite This Page:

Molecular Biology and Evolution (Oxford University Press). "New software automates and improves phylogenomics from next-generation sequencing data." ScienceDaily. ScienceDaily, 6 March 2014. <www.sciencedaily.com/releases/2014/03/140306093804.htm>.
Molecular Biology and Evolution (Oxford University Press). (2014, March 6). New software automates and improves phylogenomics from next-generation sequencing data. ScienceDaily. Retrieved October 20, 2014 from www.sciencedaily.com/releases/2014/03/140306093804.htm
Molecular Biology and Evolution (Oxford University Press). "New software automates and improves phylogenomics from next-generation sequencing data." ScienceDaily. www.sciencedaily.com/releases/2014/03/140306093804.htm (accessed October 20, 2014).

Share This



More Plants & Animals News

Monday, October 20, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

White Lion Cubs Born in Belgrade Zoo

White Lion Cubs Born in Belgrade Zoo

AFP (Oct. 20, 2014) Two white lion cubs, an extremely rare subspecies of the African lion, were recently born at Belgrade Zoo. They are being bottle fed by zoo keepers after they were rejected by their mother after birth. Duration: 00:42 Video provided by AFP
Powered by NewsLook.com
Traditional Farming Methods Gaining Ground in Mali

Traditional Farming Methods Gaining Ground in Mali

AFP (Oct. 20, 2014) He is leading a one man agricultural revolution in Mali - Oumar Diatabe uses traditional farming methods to get the most out of his land and is teaching others across the country how to do the same. Duration: 01:44 Video provided by AFP
Powered by NewsLook.com
Goliath Spider Will Give You Nightmares

Goliath Spider Will Give You Nightmares

Buzz60 (Oct. 20, 2014) An entomologist stumbled upon a South American Goliath Birdeater. With a name like that, you know it's a terrifying creepy crawler. Sean Dowling (@SeanDowlingTV) has the details. Video provided by Buzz60
Powered by NewsLook.com
Hey, Doc! Sewage, Beer and Food Scraps Can Power Chevrolet’s Bi-Fuel Impala

Hey, Doc! Sewage, Beer and Food Scraps Can Power Chevrolet’s Bi-Fuel Impala

3BL Media (Oct. 20, 2014) Hey, Doc! Sewage, Beer and Food Scraps Can Power Chevrolet’s Bi-fuel Impala Video provided by 3BL
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins