#include "customize.wml"
#use wml::Utils::template
#use wml::Utils::menu" title="ALTree
#use wml::Utils::newframe
#use wml::Utils::gettext

<div class="leftside">

<frame title="Context">
  A major question in genetic epidemiology nowadays is to find the
  genes involved in complex disease susceptibility and among those
  genes, to localize the variant sites explaining this susceptibility.
  Numerous haplotypic methods have been developped, but when the number
  of haplotypes is large, a grouping may be required so that the power of
  these analysis is not too low.  Phylogenetic trees allow such
  groupings of haplotypes based on their evolutionary history and may
  help in the detection and localization of disease susceptibility

<frame title="What is ALTree?">
  ALTree is a software which performs two phylogeny-based analysis:
    <li> it tests the association between a candidate gene and a disease</li>
    <li> it pinpoints markers (SNPs) that are putative disease
         susceptibility loci</li>
  ALTree consists is three independent programs. 
    <dt> ALTree </dt>
    <dd> the main program which performs the association and
         localization test

    <dt> ALTree-convert and ALTree-add-S </dt>
    <dd> two utilities which help the user managing its data file
    before running ALTree
  <p> The method implemented in ALTree hase been fully described in <a
      href="http://www.biomedcentral.com/1471-2156/6/24">Bardel et al,
      BMC Genet 6:24, 2005</a>


<div class="rightside">
<frame title="News">
  <dt> November 22nd 2013</dt>
  <dd> Performances of ALTree have been improved, computing time is now greatly reduced (version 1.3.0)</dd> 
  <dt> July 11th 2008</dt>
  <dd> ALTree now deals with quantitative data (version 1.1.0)</dd> 
  <dt> March 17th 2006</dt> 
  <dd> first release of ALTree (version 1.0.1)</dd>

<frame title="Download">
    <dt><a href="files/manual.pdf">ALTree manual</a>:</dt>
    <dd> The documentation file for ALTree (in pdf)</dd>

    <dt> <a href="files/">ALTree sources</a></dt>
    <dd> ALTree source files

  A debian package for ALTree can be found in
  <a href="http://packages.debian.org/altree">Debian</a>

<frame title="Needed softwares">
  To run ALTree, it is necessary to use one of these phylogeny
  reconstruction sofwares: 

  <dl class="links">
    <dt><a href="http://paup.csit.fsu.edu/">PAUP*: Phylogenetic
      Analysis Using Parsimony</a> </dt> 
    <dd> This software written by D. Swofford must be purchased 
         (100\$ for the linux version)

      PHYLogeny Inference Package</a>
    <dd> This software written by J. Felsenstein is freely available. 

      Phylogenetic Analysis by Maximum Likelihood</a>
       This software written by Z. Yang is freely available.

       This software written by S Guidon and O. Gascuel is freely available.