Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

A Format for Phylogenetic Placements

(2012) Frederick A. Matsen et al.   PLoS One

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Visualization of multiple alignments, phylogenies and gene family evolution

(2010) James B Procter et al.   NATURE METHODS

phyloXML: XML for evolutionary biology and comparative genomics

(2009) Mira V Han et al.   BMC BIOINFORMATICS

PhyloWidget: web-based visualizations for the tree of life

(2008) G. E. Jordan et al.   BIOINFORMATICS