Answers.Body: <p>ANI = average nucleotide identity.</p>
  
  <p>This will give you a 2x2 matrix. You reconstruct a phylogeny using clustering, the most important being neighbor-joining, UPGMA is very occassionally used.</p>
  
  <p>The statistic is clustering algorithm and its done by pairwise reconstruction of sister groups. Once a sister-group is defined (usually on nearest-neighor both in neighbor-joining and UPGMA) the genetic divergence from the hypothetical node is established either using the mean (UPGMA) or additive criteria (neighbor-joining). Okay enough theory ...</p>
  
  <p>You get Mega X and find out the import format for a 2x2 distance matric. Mega X however will calculate this for you. You then go to the build tree menu heading and click "neighbor-joining" (or "distance"). The tree will very quickly automatically appear.</p>
  
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Answers.Text: Thanks~ Wish you have a good day (or night???)  : )
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Answers.Text: But isn't the result of ANI is an NxN matrix? How to translate it into a 2x2 matrix? I used the dcast() funtion in R to transform the data, from A to B.
  A:
  Streptomyces_zinciresistens.fna Streptomyces_aidingensis.fna    78.6608 909     2493
  Streptomyces_zinciresistens.fna Streptomyces_gilvigriseus.fna   78.4136 719     2493
  ...
  B:
                  Kitasatospora.papulosa Streptomyces.achromogenes Streptomyces.adustus
  Kitasatospora papulosa                  100.0000                   81.0354              81.1125
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Answers.Text: Okay, first up I don't use R, I use Python instead, the only thing I'll use R for is ggplot2. I've never worked on Strep. What we should do is arrange a time to chat on the phylogenetics debugging forum
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Answers.Text: Sorry, but where is the phylogenetics debugging forum? ... I come from a web restricted area, have little knowledge about the foreign web... CRY
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Answers.Text: ??? Where is the invitation? Should I check my Gmail message box? I can't see it in stack exchange's message box
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Body: <p>I've calculated the ANI of the streptomyces genus, but I'm confused about how to separate them into a different group, could anybody kindly tell me how to do that? Thanks!!!</p>
  
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Comments.Text: Oh thats easy you use clustering analysis
Comments.UserDisplayName: M__
Tags: <phylogenetics><phylogeny>
Title: How to seperate the genus into different group based on th ANI calculation?
ThreadText: # How to seperate the genus into different group based on th ANI calculation?
  
  (Asked by: username_0 on 2020-03-08)
  
  I've calculated the ANI of the streptomyces genus, but I'm confused about how to separate them into a different group, could anybody kindly tell me how to do that? Thanks!!!
  
  **Tags:** phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: Oh thats easy you use clustering analysis  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-03-08. Score: 1 | Accepted answer
  
  ANI = average nucleotide identity.
  
  This will give you a 2x2 matrix. You reconstruct a phylogeny using clustering, the most important being neighbor-joining, UPGMA is very occassionally used.
  
  The statistic is clustering algorithm and its done by pairwise reconstruction of sister groups. Once a sister-group is defined (usually on nearest-neighor both in neighbor-joining and UPGMA) the genetic divergence from the hypothetical node is established either using the mean (UPGMA) or additive criteria (neighbor-joining). Okay enough theory ...
  
  You get Mega X and find out the import format for a 2x2 distance matric. Mega X however will calculate this for you. You then go to the build tree menu heading and click "neighbor-joining" (or "distance"). The tree will very quickly automatically appear.
  
  > **Comments:**
  > **username_0**: Thanks~ Wish you have a good day (or night???)  : )  
  > **username_0**: But isn't the result of ANI is an NxN matrix? How to translate it into a 2x2 matrix? I used the dcast() funtion in R to transform the data, from A to B. A: Streptomyces_zinciresistens.fna Streptomyces_aidingensis.fna    78.6608 909     2493 Streptomyces_zinciresistens.fna Streptomyces_gilvigriseus.fna   78.4136 719     2493 ... B:                 Kitasatospora.papulosa Streptomyces.achromogenes Streptomyces.adustus Kitasatospora papulosa                  100.0000                   81.0354              81.1125  
  > **username_1**: Okay, first up I don't use R, I use Python instead, the only thing I'll use R for is ggplot2. I've never worked on Strep. What we should do is arrange a time to chat on the phylogenetics debugging forum  
  > **username_0**: Sorry, but where is the phylogenetics debugging forum? ... I come from a web restricted area, have little knowledge about the foreign web... CRY  
  > **username_0**: Thank you!!! You are so nice !!!  
  > **username_0**: ??? Where is the invitation? Should I check my Gmail message box? I can't see it in stack exchange's message box  
  > **username_1**: Hi @username_0 really sorry I was late, if you are around the same time tomorrow please let me know  
  > **username_0**: Yes, I'll be around at the same time tomorrow, it's ok.  
  > **username_1**: Just a minute I'm in a meeting  
  > **username_0**: okkk, it'll be fine, i'll memorize the words(or recite words)  
  
  ---
  
  