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 July 31, 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 July 31, 2014).

Share This




More Plants & Animals News

Thursday, July 31, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Visitors Feel Part of the Pack at Wolf Preserve

Visitors Feel Part of the Pack at Wolf Preserve

AP (July 31, 2014) Seacrest Wolf Preserve on the northern Florida panhandle allows more than 10,000 visitors each year to get up close and personal with Arctic and British Columbian Wolves. (July 31) Video provided by AP
Powered by NewsLook.com
Florida Panther Rebound Upsets Ranchers

Florida Panther Rebound Upsets Ranchers

AP (July 31, 2014) With Florida's panther population rebounding, some ranchers complain the protected predators are once again killing their calves. (July 31) Video provided by AP
Powered by NewsLook.com
Dangerous Bacteria Kills One in Florida

Dangerous Bacteria Kills One in Florida

AP (July 31, 2014) Sarasota County, Florida health officials have issued a warning against eating raw oysters and exposing open wounds to coastal and inland waters after a dangerous bacteria killed one person and made another sick. (July 31) Video provided by AP
Powered by NewsLook.com
Raw: Thousands Flocking to German Crop Circle

Raw: Thousands Flocking to German Crop Circle

AP (July 30, 2014) Thousands of people are trekking to a Bavarian farmer's field to check out a mysterious set of crop circles. (July 30) Video provided by AP
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:
from the past week

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