SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
TLDR
SeaView version 4 combines all the functions of the widely used programs SeaView and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees.Abstract:
We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.read more
Citations
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
Fabian Sievers,Andreas Wilm,David Dineen,Toby J. Gibson,Kevin Karplus,Weizhong Li,Rodrigo Lopez,Hamish McWilliam,Michael Remmert,Johannes Söding,Julie D. Thompson,Desmond G. Higgins +11 more
TL;DR: A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality.
Journal ArticleDOI
AliView: a fast and lightweight alignment viewer and editor for large datasets
TL;DR: AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets and works as an easy-to-use alignment editor for small as well as large datasets.
Journal ArticleDOI
Building Phylogenetic Trees from Molecular Data with MEGA
TL;DR: A step-by-step protocol is presented in sufficient detail to allow a novice to start with a sequence of interest and to build a publication-quality tree illustrating the evolution of an appropriate set of homologs of that sequence.
Journal ArticleDOI
The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals
Maureen A. O'Leary,Maureen A. O'Leary,Jonathan I. Bloch,John J. Flynn,Timothy J. Gaudin,Andres Giallombardo,Norberto P. Giannini,Suzann L. Goldberg,Brian P. Kraatz,Brian P. Kraatz,Zhe-Xi Luo,Jin Meng,Xijun Ni,Michael J. Novacek,Fernando A. Perini,Zachary S. Randall,Guillermo W. Rougier,Eric J. Sargis,Mary T. Silcox,Nancy B. Simmons,Michelle Spaulding,Michelle Spaulding,Paúl M. Velazco,Marcelo Weksler,John R. Wible,Andrea L. Cirranello,Andrea L. Cirranello +26 more
TL;DR: A phylogenetic tree shows that crown clade Placentalia and placental orders originated after the K-Pg boundary, but phenomic signals overturn molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister taxon of Primates, a close link between Proboscidea and Sirenia (sea cows), and the monophyly of echolocating Chiroptera (bats).
Journal ArticleDOI
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Anja Spang,Jimmy H. Saw,Steffen Leth Jørgensen,Katarzyna Zaremba-Niedzwiedzka,Joran Martijn,Anders E. Lind,Roel van Eijk,Christa Schleper,Christa Schleper,Lionel Guy,Lionel Guy,Thijs J. G. Ettema +11 more
TL;DR: The discovery of ‘Lokiarchaeota’ is described, a novel candidate archaeal phylum which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eUKaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities.
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