Answers.Body: <p>The MLST genes are not used to contruct a tree, because each pattern of alleles determines a predetermined genotype, e.g.  Staphlococcus aureus ST 22 is the MLST type concerning the MRSA epidemic. You could build a tree, but its only purpose is to visualise the ST, so its a bit pointless but okay at least you will not mistype something.</p>
  
  <p>Performing a whole genome tree on Strep for the genus is complicated but doable and there are missing genes and stuff and if you just want typing then its not needed.</p>
  
  <hr>
  
  <p>So if typing is your goal I would submit your MLST loci to the Steptomyces MLST database,</p>
  
  <p><a href="https://pubmlst.org/bigsdb?db=pubmlst_streptomyces_seqdef" rel="nofollow noreferrer">https://pubmlst.org/bigsdb?db=pubmlst_streptomyces_seqdef</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-08T10:25:38.637Z
Answers.Text: Thanks!!! I've calculated the ANI of the streptomyces genus(only the type materials), and now I'm running the Orthomcl the get the core genes(the number of which is expected to exceed 1000), after that, I'll build the phylogenetic tree of the genus~
Answers.UserDisplayName: TANGLi83
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-08T10:43:02.503Z
Answers.Text: Could you kindly recommend some lessons or books about the phylogenetic filed for me? My major is horticulture and I've learned the basic lesson of bioinformatics and learned the Perl, Python, Linux, and R language. But I lack the professional knowledge of bioinformatics. Thanks for the help!!!!
Answers.UserDisplayName: TANGLi83
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-08T11:05:03.910Z
Answers.Text: At your level use Mega X its easy to use. There's quiet alot of info in phylogenetics theory throughout BioSE. If you get stuck you have to ask a separate question (Bio SE rules)
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-08T12:19:42.653Z
Answers.Text: Thanks for your answer, I had an Internship at a bioinformatics company, so I've run the gene family project~ I'll study in the BioSE!!! But sorry, what is biose? I can't google it...
Answers.UserDisplayName: TANGLi83
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-08T12:31:51.100Z
Answers.Text: oh, I got that now, BioSE means biology searching engine...English isn't my mother tongue...
Answers.UserDisplayName: TANGLi83
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-08T13:17:44.043Z
Answers.Text: Sorry, Bioinformatics Stackexchange has quite a few threads on phylogenetics.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-07T15:21:45.593Z
Answers.LastActivityDate: 2020-03-07T19:55:33.930Z
Answers.LastEditDate: 2020-03-07T19:55:33.930Z
Answers.UserDisplayName: M__
Body: <p>I am confused about how to construct the phylogenetic tree of the streptomyces genus. The taxonomy of the streptomyces genus is mostly based on the MLST method, but now I need to use the gene data from NCBI to construct the phylogenetic tree of the streptomyces genus. Should I use the whole gene of the MLST's housekeeping gene to construct the tree? Or I should just use the loci to build the tree? Or the other method? I am a junior in university, have little knowledge of the filed., but my tutor asked me to do that. plus: Sorry for my awkward expression~</p>
  
Tags: <phylogenetics><phylogeny>
Title: How to construct the phylogenetic tree of the whole genus?
ThreadText: # How to construct the phylogenetic tree of the whole genus?
  
  (Asked by: username_0 on 2020-03-07)
  
  I am confused about how to construct the phylogenetic tree of the streptomyces genus. The taxonomy of the streptomyces genus is mostly based on the MLST method, but now I need to use the gene data from NCBI to construct the phylogenetic tree of the streptomyces genus. Should I use the whole gene of the MLST's housekeeping gene to construct the tree? Or I should just use the loci to build the tree? Or the other method? I am a junior in university, have little knowledge of the filed., but my tutor asked me to do that. plus: Sorry for my awkward expression~
  
  **Tags:** phylogenetics, phylogeny
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-03-07. Score: 1 | Accepted answer
  
  The MLST genes are not used to contruct a tree, because each pattern of alleles determines a predetermined genotype, e.g. Staphlococcus aureus ST 22 is the MLST type concerning the MRSA epidemic. You could build a tree, but its only purpose is to visualise the ST, so its a bit pointless but okay at least you will not mistype something.
  
  Performing a whole genome tree on Strep for the genus is complicated but doable and there are missing genes and stuff and if you just want typing then its not needed.
  
  ---
  
  So if typing is your goal I would submit your MLST loci to the Steptomyces MLST database,
  
  <https://pubmlst.org/bigsdb?db=pubmlst_streptomyces_seqdef>
  
  > **Comments:**
  > **username_0**: Thanks!!! I've calculated the ANI of the streptomyces genus(only the type materials), and now I'm running the Orthomcl the get the core genes(the number of which is expected to exceed 1000), after that, I'll build the phylogenetic tree of the genus~  
  > **username_0**: Could you kindly recommend some lessons or books about the phylogenetic filed for me? My major is horticulture and I've learned the basic lesson of bioinformatics and learned the Perl, Python, Linux, and R language. But I lack the professional knowledge of bioinformatics. Thanks for the help!!!!  
  > **username_1**: At your level use Mega X its easy to use. There's quiet alot of info in phylogenetics theory throughout BioSE. If you get stuck you have to ask a separate question (Bio SE rules)  
  > **username_0**: Thanks for your answer, I had an Internship at a bioinformatics company, so I've run the gene family project~ I'll study in the BioSE!!! But sorry, what is biose? I can't google it...  
  > **username_0**: oh, I got that now, BioSE means biology searching engine...English isn't my mother tongue...  
  > **username_1**: Sorry, Bioinformatics Stackexchange has quite a few threads on phylogenetics.  
  
  ---
  
  