Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tiger genome and comparative analysis with lion and snow leopard genomes

(2013) Yun Sung Cho et al.   Nature Communications

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

(2012) Ari Löytynoja et al.   BIOINFORMATICS

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web

(2010) Samuel A. Smits et al.   PLoS One

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Extended Newick: it is time for a standard representation of phylogenetic networks

(2009) Gabriel Cardona et al.   BMC BIOINFORMATICS

phyloXML: XML for evolutionary biology and comparative genomics

(2009) Mira V Han et al.   BMC BIOINFORMATICS

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

A model of evolution and structure for multiple sequence alignment

(2008) A. Loytynoja et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE