<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>

CC BY-SA 4.0
2020-06-04T03:30:17.863Z
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.
Mendel
CC BY-SA 4.0
2020-06-04T03:39:27.817Z
And how I can calculate mutation rates?
Mendel
CC BY-SA 4.0
2020-06-05T20:20:03.233Z
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
Nicholas Heyer
CC BY-SA 4.0
2020-06-02T23:21:17.160Z
2020-06-02T23:21:17.160Z
Nicholas Heyer
<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>

CC BY-SA 4.0
2020-06-08T13:04:54.917Z
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).
Kamil S Jaron
CC BY-SA 4.0
2020-06-11T00:54:12.020Z
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
Bioathlete
<phylogenetics><covid-19><mutations><sars-cov-2><virus>
How to calculate mutation rate and mutation sites in a genome using FASTA file?
# 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  

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## 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  

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