Answers.Body: <p>You can still align a FASTA file with a tool like <a href="https://github.com/lh3/bwa" rel="nofollow noreferrer">bwa mem</a> ( if they are short reads ) or <a href="https://github.com/lh3/minimap2" rel="nofollow noreferrer">minimap2</a> for long reads and run it through a variant caller like <a href="https://github.com/ekg/freebayes" rel="nofollow noreferrer">freebayes</a>. Alternatively, if you have sufficient reads to create an assembly of all of the genomes, or if they already are you can create a MSA of them using a tool like <a href="https://github.com/ComparativeGenomicsToolkit/cactus" rel="nofollow noreferrer">Cactus</a> (as it is built for genomes) or MAFFT if the sequences are short enough and then use your favorite viewer to find variable sites </p>
  
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Answers.CreationDate: 2020-06-04T03:30:17.863Z
Answers.Text: I've assembled genome and the genome size is about 30-32k, so I align them and after that, I try to check variable region, It will take a lot of time.
Answers.UserDisplayName: Mendel
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Answers.CreationDate: 2020-06-04T03:39:27.817Z
Answers.Text: And how I can calculate mutation rates?
Answers.UserDisplayName: Mendel
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-05T20:20:03.233Z
Answers.Text: I don't expect it to take too long to run as MAFFT i-INS-n ( mush slower then Cactus but probably more accurate)  can align my dateset of 208 seq at 200kb  in around 20000 clock hours  (20 hrs with 10 cores ) so 6 should be fine unless they are really gappy.  I am unclear what you mean about mutation rates in this context unless these genomes have established time points
Answers.UserDisplayName: Nicholas Heyer
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Answers.CreationDate: 2020-06-02T23:21:17.160Z
Answers.LastActivityDate: 2020-06-02T23:21:17.160Z
Answers.UserDisplayName: Nicholas Heyer
Body: <p>I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format.</p>
  <ol>
  <li>How I can identify mutations and mutation sites in those genomes using FASTA sequences  but how I can do this for FASTA file?</li>
  <li>And how I can identify the mutation rate for one genome?</li>
  </ol>
  <p><strong>Background</strong> If I've FASTQ file then I'll simply align the reads to the reference and by using variant calling tool I will get the mutate sites</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-08T13:04:54.917Z
Comments.Text: The mutation rate is impossible to calculate without knowing when the samples diverged. If you have fasta sequences, you can align them and build a tree (I guess beast is the most common tool for viral genomes including time calibration).
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-11T00:54:12.020Z
Comments.Text: Typically you can align FASTA or FASTQ sequences.  If your variant caller of choice doesn't accept a FASTA and you trust the bases in your FASTA you could mock up the quality scores and make a FASTQ
Comments.UserDisplayName: Bioathlete
Tags: <phylogenetics><covid-19><mutations><sars-cov-2><virus>
Title: How to calculate mutation rate and mutation sites in a genome using FASTA file?
ThreadText: # How to calculate mutation rate and mutation sites in a genome using FASTA file?
  
  (Asked by: username_0 on 2020-06-01)
  
  I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format.
  
  1. How I can identify mutations and mutation sites in those genomes using FASTA sequences but how I can do this for FASTA file?
  2. And how I can identify the mutation rate for one genome?
  
  **Background** If I've FASTQ file then I'll simply align the reads to the reference and by using variant calling tool I will get the mutate sites
  
  **Tags:** phylogenetics, covid-19, mutations, sars-cov-2, virus
  
  > **Comments:**
  > **username_1**: The mutation rate is impossible to calculate without knowing when the samples diverged. If you have fasta sequences, you can align them and build a tree (I guess beast is the most common tool for viral genomes including time calibration).  
  > **username_2**: Typically you can align FASTA or FASTQ sequences.  If your variant caller of choice doesn't accept a FASTA and you trust the bases in your FASTA you could mock up the quality scores and make a FASTQ  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2020-06-02. Score: 1
  
  You can still align a FASTA file with a tool like [bwa mem](https://github.com/lh3/bwa) ( if they are short reads ) or [minimap2](https://github.com/lh3/minimap2) for long reads and run it through a variant caller like [freebayes](https://github.com/ekg/freebayes). Alternatively, if you have sufficient reads to create an assembly of all of the genomes, or if they already are you can create a MSA of them using a tool like [Cactus](https://github.com/ComparativeGenomicsToolkit/cactus) (as it is built for genomes) or MAFFT if the sequences are short enough and then use your favorite viewer to find variable sites
  
  > **Comments:**
  > **username_0**: I've assembled genome and the genome size is about 30-32k, so I align them and after that, I try to check variable region, It will take a lot of time.  
  > **username_0**: And how I can calculate mutation rates?  
  > **username_3**: I don't expect it to take too long to run as MAFFT i-INS-n ( mush slower then Cactus but probably more accurate)  can align my dateset of 208 seq at 200kb  in around 20000 clock hours  (20 hrs with 10 cores ) so 6 should be fine unless they are really gappy.  I am unclear what you mean about mutation rates in this context unless these genomes have established time points  
  
  ---
  
  