Phylogenesis

  • Datum: 28.12.15

  • = Phylogenetics. Backgroundinformation and software regarding maximum likelihood and bayesian evolutionary analysis, phylogenetic trees and networks.

General

Phylogenetic Trees

Background

Doyle, J.J., 1995. The Irrelevance of Allele Tree Topologies for Species Delimitation, and a Non-Topological Alternative. Systematic Botany, 20(4), pp.574–588.
Available at: http://europepmc.org/abstract/AGR/IND20522043.

Software

  • FigTree
    • Homepage: http://tree.bio.ed.ac.uk/software/figtree/
    • Description: "FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST."
  • Archaeopteryx
    • Homepage: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx
    • Publication (of the predecessor): Zmasek, C.M. & Eddy, S.R., 2001. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics, 17(4), pp.383–384.
      http://bioinformatics.oxfordjournals.org/content/17/4/383.abstract
    • Description: "Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. Archaeopteryx (the successor to ATV) is entirely written in the Java programming language (it is based on the forester libraries). It can be used both as a standalone application and as applet (ArchaeopteryxA and ArchaeopteryxE)."
  • GraPhlAn

 

Maximum Likelihood Analysis

Background

Software

  • PAML (for Phylogenetic Analysis by Maximum Likelihood)
    • Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
    • Publication: Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8), 1586–91. http://doi.org/10.1093/molbev/msm088
    • Description: "PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations."

Bayesian Analysis

Background

Software

  • BEAST - Bayesian Evolutionary Analysis Sampling Trees
    • Homepage: http://beast.bio.ed.ac.uk/
    • Publication: Drummond, A.J. et al., 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular biology and evolution, 29(8), pp.1969–73. 
      http://mbe.oxfordjournals.org/content/29/8/1969.
    • Description: "BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results."
       
  • MrBayes - Bayesian Inference of Phylogeny
    • Homepage: http://mrbayes.sourceforge.net/
    • Publication: Ronquist, F. et al., 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology, 61(3), pp.539–42.
      http://sysbio.oxfordjournals.org/content/61/3/539.
    • Description: "MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters."

Phylogenetic Networks

Background

 

Software

  • Splits Tree
    • Homepage: http://www.splitstree.org/
    • Publication: Huson, D. H., & Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23(2), 254–67. http://doi.org/10.1093/molbev/msj030
    • Description: "SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks."