Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-17T05:24:29.353Z
Answers.LastActivityDate: 2019-08-17T16:25:52.337Z
Answers.LastEditDate: 2019-08-17T16:25:52.337Z
Answers.UserDisplayName: M__
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-14T12:27:29.807Z
Comments.Text: Can you give us some example data? It's kind of hard to understand what you're looking at. Are you trying to build a phylogeny based on the entire cluster or have you separated each species' cluster into a multifasta file with each gene separate? If you haven't, wouldn't that be a reasonable approach?
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2019-08-14T13:41:13.277Z
Comments.Text: If there'd be a way to build a phylogeny based on the entire cluster (that can deal with indels/inversions/rearrangements), I'd love to know it.
  
  I guess I could separate each species' cluster into a multifasta file, but I'm not sure what I could do after that? Could you please explain? It's unfortunate, because I'd lose positional information (eg. let's say species X is closely related to species Y and less so to species Z. In X and Y, the genes are in the order A-B-C-D, in Z they're in the order A-D-C-B), but if it's the only way...
Comments.UserDisplayName: Laura
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Comments.CreationDate: 2019-08-14T17:48:53.317Z
Comments.Text: Well, I don't really think the order will make much of a change in the phylogeny. I'd just use the multifasta approach to build the tree and then maybe annotate it with the directionality.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2019-08-14T18:10:29.683Z
Comments.Text: Its easy ... I strongly suspect these are bacteria ...please confirm. The likely application is resistance cassettes again please confirm. Finally this is likely a "genetic island" rather than a single gene ... again please confirm.
Comments.UserDisplayName: M__
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Comments.CreationDate: 2019-08-15T09:48:31.527Z
Comments.Text: @terdon - Thank you. I've never built trees with multiple genes at a time, before. Could you recommend some software for it, please? Until now I've mostly used Seaview and the CIPRES webserver.
Comments.UserDisplayName: Laura
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Comments.CreationDate: 2019-08-15T09:48:39.330Z
Comments.Text: @Michael G. - Bacteria, yes. (Silly me, forgot to specify); resistance cassettes, no. And, yes I'm talking of a group of genes rather than a single gene.
Comments.UserDisplayName: Laura
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-15T16:19:34.317Z
Comments.Text: How many taxa? 1000s or <100 that is kinda important. I get the idea the fragment is 20-30 kb
Comments.UserDisplayName: M__
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Comments.CreationDate: 2019-08-16T12:14:48.100Z
Comments.Text: @MichaelG. Around 20 taxa.
Comments.UserDisplayName: Laura
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-16T12:21:39.363Z
Comments.Text: Oh that's easy. I'll post a full response later/tomorrow if no one else does.
Comments.UserDisplayName: M__
Tags: <fasta><phylogenetics><gene><phylogeny><pathway>
Title: Are there any resources for calculating / representing evolutionary relationships within gene clusters?
ThreadText: # Are there any resources for calculating / representing evolutionary relationships within gene clusters?
  
  (Asked by: username_0 on 2019-08-14)
  
  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!
  
  **Tags:** fasta, phylogenetics, gene, phylogeny, pathway
  
  > **Comments:**
  > **username_1**: Can you give us some example data? It's kind of hard to understand what you're looking at. Are you trying to build a phylogeny based on the entire cluster or have you separated each species' cluster into a multifasta file with each gene separate? If you haven't, wouldn't that be a reasonable approach?  
  > **username_0**: If there'd be a way to build a phylogeny based on the entire cluster (that can deal with indels/inversions/rearrangements), I'd love to know it.  I guess I could separate each species' cluster into a multifasta file, but I'm not sure what I could do after that? Could you please explain? It's unfortunate, because I'd lose positional information (eg. let's say species X is closely related to species Y and less so to species Z. In X and Y, the genes are in the order A-B-C-D, in Z they're in the order A-D-C-B), but if it's the only way...  
  > **username_1**: Well, I don't really think the order will make much of a change in the phylogeny. I'd just use the multifasta approach to build the tree and then maybe annotate it with the directionality.  
  > **username_2**: Its easy ... I strongly suspect these are bacteria ...please confirm. The likely application is resistance cassettes again please confirm. Finally this is likely a "genetic island" rather than a single gene ... again please confirm.  
  > **username_0**: @username_1 - Thank you. I've never built trees with multiple genes at a time, before. Could you recommend some software for it, please? Until now I've mostly used Seaview and the CIPRES webserver.  
  > **username_0**: @Michael G. - Bacteria, yes. (Silly me, forgot to specify); resistance cassettes, no. And, yes I'm talking of a group of genes rather than a single gene.  
  > **username_2**: How many taxa? 1000s or <100 that is kinda important. I get the idea the fragment is 20-30 kb  
  > **username_0**: @MichaelG. Around 20 taxa.  
  > **username_2**: Oh that's easy. I'll post a full response later/tomorrow if no one else does.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-08-17. Score: 1
  
  Firstly you wanted a webserver to build a tree, ok, I would use [PhyML server](http://www.atgc-montpellier.fr/phyml/). 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?
  
  
  ---
  
  