title: Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists
author:  Barry G. Hall 
description: This text is intended to aid beginners in getting started creating phylogenetic trees from protein or nucleic acid sequence data. Although aimed at molecular and cell biologists who may not be familiar with phylogenetic or evolutionary theory, it also serves students who may be familiar with phylogenetic theory but unfamiliar with the tools used to apply that theory. The reader is led, step-by-step, through identifying sequences that are homologous to a sequence of interest, downloading those sequences from databases, creating multiple alignments, and using several different methods to construct trees.
zlib_text: ORIGINAL PAPER
  Molecular characterization of cold adaptation based on ortholog
  protein sequences from Vibrionaceae species
  Steinar Thorvaldsen Æ Erik Hjerde Æ Chris Fenton Æ
  Nils P. Willassen
  Received: 14 November 2006 / Accepted: 15 May 2007 / Published online: 19 June 2007
  � Springer 2007
  Abstract
  A set of 298 protein families from psychrophilic
  Vibrio salmonicida was compiled to identify genotypic
  characteristics that discern it from orthologous sequences
  from the mesophilic Vibrio/Photobacterium branch of the
  gamma-Proteobacteria (Vibrionaceae family). In our com-
  parative exploration we employed alignment based bioin-
  formatical and statistical methods. Interesting information
  was found in the substitution matrices, and the pattern
  of asymmetries in the amino acid substitution process.
  Together with the compositional difference, they identiﬁed
  the amino acids Ile, Asn, Ala and Gln as those having the
  most psycrophilic involvement. Ile and Asn are enhanced
  whereas Gln and Ala are s