Answers.Body: <p>If you have <em>de novo</em> assembled genomes you can perform a pairwise whole-genome alignment, MUMmer4 is a good choice. The command <code>nucmer</code> can align the assemblies while <code>show-snps</code> extracts the polymorphisms between them.</p>
  <p>Here is the link to MUMmer: <a href="https://github.com/mummer4/mummer/tree/master" rel="nofollow noreferrer">https://github.com/mummer4/mummer/tree/master</a></p>
  <p>ProgressiveMauve and Cactus are also good choices if you need multiple whole-genome alignments. Note that ProgressiveMauve is no longer maintained.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-05T16:36:42.820Z
Answers.LastActivityDate: 2024-11-05T16:41:22.977Z
Answers.LastEditDate: 2024-11-05T16:41:22.977Z
Answers.UserDisplayName: nicolotellini
Body: <p>I am relatively new here. I am looking for a tool that can retrieve all divergent regions between two strains of E.coli into a different file. I also wanted to be sure that using global alignment would be the most appropriate.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-31T15:22:57.177Z
Comments.Text: Please [edit] your question and add more detail. Are we talking about nucleotide or amino acid alignments? How do you define "divergent"? Is this an alignment of two sequences or multiple pairwise alignments? Have aligned an entire genome? One gene? Many genes? What is the alignment file format you are using? What operating system does this tool need to run on?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-10-31T18:19:52.470Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Tags: <phylogenetics><genome><biopython><pairwise>
Title: retrieving divergent regions of a pairwise alignment
ThreadText: # retrieving divergent regions of a pairwise alignment
  
  (Asked by: username_0 on 2024-10-31)
  
  I am relatively new here. I am looking for a tool that can retrieve all divergent regions between two strains of E.coli into a different file. I also wanted to be sure that using global alignment would be the most appropriate.
  
  **Tags:** phylogenetics, genome, biopython, pairwise
  
  > **Comments:**
  > **username_1**: Please [edit] your question and add more detail. Are we talking about nucleotide or amino acid alignments? How do you define "divergent"? Is this an alignment of two sequences or multiple pairwise alignments? Have aligned an entire genome? One gene? Many genes? What is the alignment file format you are using? What operating system does this tool need to run on?  
  > **username_2**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2024-11-05. Score: 1
  
  If you have *de novo* assembled genomes you can perform a pairwise whole-genome alignment, MUMmer4 is a good choice. The command `nucmer` can align the assemblies while `show-snps` extracts the polymorphisms between them.
  
  Here is the link to MUMmer: <https://github.com/mummer4/mummer/tree/master>
  
  ProgressiveMauve and Cactus are also good choices if you need multiple whole-genome alignments. Note that ProgressiveMauve is no longer maintained.
  
  
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