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!!!
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$\begingroup$ Oh thats easy you use clustering analysis $\endgroup$– M__ ♦Commented Mar 8, 2020 at 13:21
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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.
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$\begingroup$ Thanks~ Wish you have a good day (or night???) : ) $\endgroup$– TANGLi83Commented Mar 8, 2020 at 14:03
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$\begingroup$ 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 $\endgroup$– TANGLi83Commented Mar 8, 2020 at 14:08
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$\begingroup$ 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 $\endgroup$– M__ ♦Commented Mar 8, 2020 at 14:11
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$\begingroup$ Sorry, but where is the phylogenetics debugging forum? ... I come from a web restricted area, have little knowledge about the foreign web... CRY $\endgroup$– TANGLi83Commented Mar 8, 2020 at 14:19
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1$\begingroup$ okkk, it'll be fine, i'll memorize the words(or recite words) $\endgroup$– TANGLi83Commented Mar 11, 2020 at 14:18