PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/.

[1]  Eric Durand,et al.  apTreeshape: statistical analysis of phylogenetic tree shape , 2006, Bioinform..

[2]  B. Larget,et al.  Bayesian estimation of concordance among gene trees. , 2006, Molecular biology and evolution.

[3]  M. P. Cummings PHYLIP (Phylogeny Inference Package) , 2004 .

[4]  Luke J. Harmon,et al.  GEIGER: investigating evolutionary radiations , 2008, Bioinform..

[5]  A. King,et al.  Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution , 2004, The American Naturalist.

[6]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[7]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[8]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[9]  M. Sanderson Paloverde: an OpenGL 3D phylogeny browser , 2006, Bioinform..

[10]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[11]  Casey W. Dunn,et al.  Phyutility: a phyloinformatics tool for trees, alignments and molecular data , 2008, Bioinform..

[12]  D. Pearl,et al.  Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. , 2007, Systematic biology.

[13]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[14]  Michael J. Sanderson,et al.  Paloverde: an OpenGL 3D phylogeny browser , 2006, Bioinform..

[15]  Michael J. Sanderson,et al.  R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock , 2003, Bioinform..

[16]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[17]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[18]  Burkhard Morgenstern,et al.  DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignment , 1999, German Conference on Bioinformatics.

[19]  Derrick J. Zwickl Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion , 2006 .

[20]  D. Posada jModelTest: phylogenetic model averaging. , 2008, Molecular biology and evolution.

[21]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[22]  Christopher J. Lee,et al.  Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems , 2004, Bioinform..

[23]  Jeffrey Chang,et al.  Biopython: Python tools for computational biology , 2000, SIGB.

[24]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[25]  Rodrigo Lopez,et al.  Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..

[26]  Jean Thioulouse,et al.  The ade4 package - I : One-table methods , 2004 .

[27]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

[28]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[29]  Campbell O. Webb,et al.  Bioinformatics Applications Note Phylocom: Software for the Analysis of Phylogenetic Community Structure and Trait Evolution , 2022 .

[30]  Manolo Gouy,et al.  SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny , 1996, Comput. Appl. Biosci..

[31]  D. Maddison,et al.  Mesquite: a modular system for evolutionary analysis. Version 2.6 , 2009 .