<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>

CC BY-SA 4.0
2020-03-08T14:03:45.890Z
Thanks~ Wish you have a good day (or night???)  : )
TANGLi83
CC BY-SA 4.0
2020-03-08T14:08:38.013Z
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
TANGLi83
CC BY-SA 4.0
2020-03-08T14:11:42.543Z
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
M__
CC BY-SA 4.0
2020-03-08T14:19:41.373Z
Sorry, but where is the phylogenetics debugging forum? ... I come from a web restricted area, have little knowledge about the foreign web... CRY
TANGLi83
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2020-03-08T14:22:27.790Z
Thank you!!! You are so nice !!!
TANGLi83
CC BY-SA 4.0
2020-03-08T14:25:37.037Z
??? Where is the invitation? Should I check my Gmail message box? I can't see it in stack exchange's message box
TANGLi83
CC BY-SA 4.0
2020-03-11T13:33:10.840Z
Hi @Tangli83 really sorry I was late, if you are around the same time tomorrow please let me know
M__
CC BY-SA 4.0
2020-03-11T14:11:23.957Z
Yes, I'll be around at the same time tomorrow, it's ok.
TANGLi83
CC BY-SA 4.0
2020-03-11T14:14:01.910Z
Just a minute I'm in a meeting
M__
CC BY-SA 4.0
2020-03-11T14:18:21.957Z
okkk, it'll be fine, i'll memorize the words(or recite words)
TANGLi83
CC BY-SA 4.0
2020-03-08T13:27:44.743Z
2020-03-08T13:27:44.743Z
M__
<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>

CC BY-SA 4.0
2020-03-08T13:21:52.620Z
Oh thats easy you use clustering analysis
M__
<phylogenetics><phylogeny>
How to seperate the genus into different group based on th ANI calculation?
# 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 @Tangli83 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)  

---

