text: user4401: I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just do a multiple alignment of the whole cluster. I've done phylogenies of individual genes and I've looked at cluster architecture (indels, rearrangements) and things make sense (eg. limited HGT), but..
  ...Is there a simpler way to do this? A way to calculate / represent a phylogeny of the whole cluster? Like...some sort of web, maybe? Most of the software that does take rearrangements into consideration is meant for whole genomes, and is unreliable when it comes to fragments about 20-30kb long (like mine).
  Thank you for your help!
  
  user3848: Firstly you wanted a webserver to build a tree, ok, I would use PhyML server. The good thing is that with only 22 taxa the calculations are easily doable. 
  What I'm assuming is you can map your rearrangements to produce a single homologous gene alignment for all taxa. So you appear to infer you can break your 20-30kb contig into individual aligments of homologous genes which has incorporated the rearrangement and enables easy production of an alignment file. This would leave you with around 20-30 gene alignment files. I hope that is correct, because that is how you get around the rearrangement problem and enables the data to be reassembled for the final tree (below).
  Doing the tree is simple, because you can exploit the assumptions used in tree building regarding independence between mutations at each alignment position. The theoretical proof, the data is sound, is complicated. In summary,
  
  build a consensus phylogeny (one tree representative of lots of trees) using two different approaches
  combine the data into a single alignment, if the above looks good, or excluding the alignments that are affected recombination.
  
  The theoretical issues with what you want to do are complicated because you need to distinguish bifurcating (clonal) homologues from recombination that could have occured in the reassortment events. The following is a  purists approach, you might not want to do this stuff, but it gives you some idea.
  Just before I do that ... I just want to check the alignments assumption is correct? and which bacteria?
  
original_text: 4401: <p>I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just do a multiple alignment of the whole cluster. I've done phylogenies of individual genes and I've looked at cluster architecture (indels, rearrangements) and things make sense (eg. limited HGT), but..</p>
  
  <p>...Is there a simpler way to do this? A way to calculate / represent a phylogeny of the whole cluster? Like...some sort of web, maybe? Most of the software that does take rearrangements into consideration is meant for whole genomes, and is unreliable when it comes to fragments about 20-30kb long (like mine).</p>
  
  <p>Thank you for your help!</p>
   3848: <p>Firstly you wanted a webserver to build a tree, ok, I would use <a href="http://www.atgc-montpellier.fr/phyml/" rel="nofollow noreferrer">PhyML server</a>. The good thing is that with only 22 taxa the calculations are easily doable. </p>
  
  <p>What I'm assuming is you can map your rearrangements to produce a single homologous gene alignment for all taxa. So you appear to infer you can break your 20-30kb contig into individual aligments of homologous genes which has incorporated the rearrangement and enables easy production of an alignment file. This would leave you with around 20-30 gene alignment files. I hope that is correct, because that is how you get around the rearrangement problem and enables the data to be reassembled for the final tree (below).</p>
  
  <p>Doing the tree is simple, because you can exploit the assumptions used in tree building regarding independence between mutations at each alignment position. The theoretical proof, the data is sound, is complicated. In summary,</p>
  
  <ul>
  <li>build a consensus phylogeny (one tree representative of lots of trees) using two different approaches</li>
  <li>combine the data into a single alignment, if the above looks good, or excluding the alignments that are affected recombination.</li>
  </ul>
  
  <p>The theoretical issues with what you want to do are complicated because you need to distinguish bifurcating (clonal) homologues from recombination that could have occured in the reassortment events. The following is a  purists approach, you might not want to do this stuff, but it gives you some idea.</p>
  
  <p>Just before I do that ... I just want to check the alignments assumption is correct? and which bacteria?</p>
  