Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
AliView: a fast and lightweight alignment viewer and editor for large data sets
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
2014 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, no 22, 3276-3278 p.Article in journal (Refereed) Published
Abstract [en]

Summary: AliView is an alignment viewer and editor designed tomeet the requirements of next generation sequencing era phyloge-netic datasets. AliView handles alignments of unlimited size in theformats most commonly used, i.e. Fasta, Phylip, Nexus, Clustal andMSF. The intuitive graphical interface makes it easy to inspect, sort,delete, merge and realign sequences as part of the manual filteringprocess of large data sets. AliView also works as an easy to usealignment editor for small as well as large data sets.Availability: AliView is released as open-source software under theGNU General Public License, version 3.0 (GPLv3), and is availableat GitHub (www.github.com/AliView). The program is cross-platformand extensively tested on Linux, Mac OS X and Windows systems.Downloads and help are available at http://ormbunkar.se/aliviewContact: anders.larsson@ebc.uu.seSupplementary information:

Place, publisher, year, edition, pages
2014. Vol. 30, no 22, 3276-3278 p.
National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics
Identifiers
URN: urn:nbn:se:uu:diva-232231DOI: 10.1093/bioinformatics/btu531ISI: 000344774600022OAI: oai:DiVA.org:uu-232231DiVA: diva2:747140
Funder
Swedish Research Council Formas, 2006-429 and 2010-585
Available from: 2014-09-15 Created: 2014-09-15 Last updated: 2017-12-05Bibliographically approved
In thesis
1. Systematics of Woodsia: Ferns, bioinformatics and more
Open this publication in new window or tab >>Systematics of Woodsia: Ferns, bioinformatics and more
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Ferns are one of the three main clades of vascular plants. They have few easily studied morphological characters, reflected in a historically unstable classification. The fern genus Woodsia is known to have a complex evolutionary history including numerous polyploid taxa and hybrids. It is a cosmopolitan group of small rock loving ferns mainly found in montane areas.

This thesis aims at analyzing the patterns of diploid and polyploid evolution in Woodsia and to resolve and classify the relationships of Woodsiaceae and the other families in the large fern clade Eupolypods II.

The Eupolypods II family relationships were inferred with DNA sequences from 81 specimens representing all major lineages. This resulted in the first well supported phylogeny of this clade and revealed Woodsiaceae to be non-monophyletic. The genera previously placed in this family were reclassified into five new or resurrected families. Swedish fern genera that have changed family classification are Woodsia (hällebräknar), now in the monogeneric family Woodsiaceae, Athyrium (majbräknar), now  in Athyriaceeae and Cystopteris (stenbräknar) and Gymnocarpium (ekbräknar) now in Cystopteridaceae.

To analyze the evolution of Woodsia, phylogenies were produced from five plastid and two nuclear regions sequenced from 188 specimens. The results show that most taxa in Woodsia are polyploid. Polyploidization is the most common mode of speciation in the genus with an estimated polyploid speciation rate of 54%. The polyploids are mostly young and many of the polyploid taxa seem to have formed multiple times. The results also address several taxonomic and biogeographic questions.

In the process of the work we made methodological advancements and developed 20 new low copy nuclear marker regions as well as a software pipeline for finding primers in transcriptome datasets. The alignment editor software AliView was developed for handling the increasing size datasets in a user friendly way.

In conclusion this thesis provides new insights into the complexities of the evolution of a fern genus in which much of the diversity is accommodated in young species formed through polyploidization. It provides a framework of phylogenetic relationships at different levels that both answers long standing questions and generates new ones.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 36 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1182
Keyword
ferns, Eupolypods II, Woodsia, phylogeny, biogeography, polyploidy, polyploid speciation, classification, alignment
National Category
Biological Systematics
Research subject
Biology with specialization in Systematics
Identifiers
urn:nbn:se:uu:diva-232233 (URN)978-91-554-9040-9 (ISBN)
Public defence
2014-10-31, Lindahlsalen, Norbyvägen 18B, Uppsala, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council Formas, 2006-429 and 2010-585
Available from: 2014-10-10 Created: 2014-09-15 Last updated: 2015-01-23

Open Access in DiVA

fulltext(155 kB)124 downloads
File information
File name FULLTEXT01.pdfFile size 155 kBChecksum SHA-512
ea3ea89058bd2b65bbc42969966c5e568f882514e13c3a025a84f92c81185be701024bf0ace863b1748bd84ec04a2e997ad0164df94fab22e065c68ff934c415
Type fulltextMimetype application/pdf

Other links

Publisher's full texthttp://dx.doi.org/10.1093/bioinformatics/btu531
By organisation
Department of Organismal Biology
In the same journal
Bioinformatics
Bioinformatics and Systems Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 124 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 489 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf