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 25, 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 25, 2014).

Share This




More Plants & Animals News

Friday, July 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

How to Make Single Serving Smoothies: Howdini Hacks

How to Make Single Serving Smoothies: Howdini Hacks

Howdini (July 24, 2014) Smoothies are a great way to get in lots of healthy ingredients, plus they taste great! Howdini has a trick for making the perfect single-size smoothie that will save you time on cleanup too! All you need is a blender and a mason jar. Video provided by Howdini
Powered by NewsLook.com
Boy Attacked by Shark in Florida

Boy Attacked by Shark in Florida

Reuters - US Online Video (July 24, 2014) An 8-year-old boy is bitten in the leg by a shark while vacationing at a Florida beach. Linda So reports. Video provided by Reuters
Powered by NewsLook.com
Goma Cheese Brings Whiff of New Hope to DRC

Goma Cheese Brings Whiff of New Hope to DRC

Reuters - Business Video Online (July 24, 2014) The eastern region of the Democratic Republic of Congo, mainly known for conflict and instability, is an unlikely place for the production of fine cheese. But a farm in the village of Masisi, in North Kivu is slowly transforming perceptions of the area. Known simply as Goma cheese, the Congolese version of Dutch gouda has gained popularity through out the region. Ciara Sutton reports. Video provided by Reuters
Powered by NewsLook.com
Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Newsy (July 24, 2014) A new study claims a set of prehistoric T-Rex footprints supports the theory that the giant predators hunted in packs instead of alone. Video provided by Newsy
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