phyloGenerator: an automated phylogeny generation tool for ecologists

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

Building megaphylogenies for macroecology: taking up the challenge

(2012) Cristina Roquet et al.   ECOGRAPHY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

(2012) Carlo Ricotta et al.   OECOLOGIA

Measuring the distance between multiple sequence alignments

(2011) B. P. Blackburne et al.   BIOINFORMATICS

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees

(2011) Fernando Izquierdo-Carrasco et al.   BMC BIOINFORMATICS

The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences

(2011) Ralph S Peters et al.   BMC BIOLOGY

Estimating phylogenies for species assemblages: A complete phylogeny for the past and present native birds of New Zealand

(2011) Robert Lanfear et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

(2009) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

The merging of community ecology and phylogenetic biology

(2009) Jeannine Cavender-Bares et al.   ECOLOGY LETTERS

Phylocom: software for the analysis of phylogenetic community structure and trait evolution

(2008) Campbell O. Webb et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Emerging patterns in the comparative analysis of phylogenetic community structure

(2008) S. M. VAMOSI et al.   MOLECULAR ECOLOGY

GenBank

(2008) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH