Answers.Body: <p>Ah wait you mentioned a branch sites test, right that makes sense. You've got two or more identical sequences in the analysis. Ensure there are no identical sequences in your alignments and ... PRESTO! It will work :-)</p>
  <p>Below are my original thoughts before I re-read your question. I've kept the notes because it helps explain the theory a bit. There is no need to supply the tree, it should be resolved.</p>
  <hr />
  <p>The tree likelihood looks to be decreasing nicely, so it can see both the tree and the codons in the alignment.</p>
  <p>At a guess the error relates to two or more indentical nucleotide sequences in your alignment. Thus zero non-synonymous sites (amino acid change) and zero synonymous (silent) sites. This error would only occur if you were calculating selection for each 'node' in the tree (internal branch).  Alternatively, possibly if the number of synonymous sites was zero, regardless of the non-synonymous mutations this error could appear, but this doesn't seem to fit the error output.</p>
  <p>I don't know &quot;Godon&quot;, but recommend <code>PAML</code> for this analysis. Admittedly it is complicated to deploy, but it is a very robust algorithm and hugely respected.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-12T01:48:19.120Z
Answers.LastActivityDate: 2020-10-12T01:54:58.687Z
Answers.LastEditDate: 2020-10-12T01:54:58.687Z
Answers.UserDisplayName: M__
Body: <p>I am using <code>godon</code> to find genes under positive selection with the <strong>branch-site test</strong>. However, after running for a little while I get the error <em>&quot;panic: division of zero by zero or infinity by infinity&quot;</em>.</p>
  <p>Below is the full output with the error report. I can supply the phylogenetic tree and fasta file I am using if that would be helpful. Thank you.</p>
  <blockquote>
  <p>iter=33 lnL=-73104.072<br />
  iter=66 lnL=-72956.855<br />
  iter=99 lnL=-72912.956<br />
  iter=131 lnL=-72902.900<br />
  iter=162 lnL=-72900.147<br />
  iter=194 lnL=-72898.562<br />
  iter=226 lnL=-72897.970<br />
  iter=258 lnL=-72897.651<br />
  iter=289 lnL=-72897.435<br />
  iter=321 lnL=-72897.284<br />
  iter=353 lnL=-72897.199<br />
  iter=385 lnL=-72897.153<br />
  iter=416 lnL=-72897.108<br />
  iter=448 lnL=-72897.076<br />
  iter=17 lnL=-72890.551<br />
  panic: division of zero by zero or infinity by infinity
  goroutine 1 [running]:
  math/big.(*Float).Quo(0xc4273a8f40, 0xc4273a8f68, 0xc4273a8f18, 0xc42e88c118)
  /usr/local/go/src/math/big/float.go:1639 +0x15c
  bitbucket.org/Davydov/godon/cmodel.(*BranchSite).BEBPosterior(0xc422164120, 0xc4259bb900, 0x91, 0x91)
  /go/src/bitbucket.org/Davydov/godon/cmodel/bs.go:416 +0x6e9
  bitbucket.org/Davydov/godon/cmodel.(*BranchSite).Final(0xc422164120, 0x101)
  /go/src/bitbucket.org/Davydov/godon/cmodel/bs.go:455 +0x112
  main.computeFinal(0x1f263a0, 0xc422164120, 0xc4201522a0, 0x101, 0x6a80, 0x0)
  /go/src/bitbucket.org/Davydov/godon/godon/optimize.go:150 +0x93
  main.performSingleTest(0xc420162320, 0xc428266000, 0x9399, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
  /go/src/bitbucket.org/Davydov/godon/godon/hyptest.go:335 +0x1b52
  main.hypTest(0x1ee03a7, 0x1ee03a7, 0x4, 0xc4201aa501, 0x1, 0x1)
  /go/src/bitbucket.org/Davydov/godon/godon/hyptest.go:88 +0x71a
  main.main()
  /go/src/bitbucket.org/Davydov/godon/godon/godon.go:316 +0xefa</p>
  </blockquote>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-02T12:56:49.273Z
Comments.Text: Hi, sorry about delay. Apparently I didn't subscribe properly to the tag.  Anyhow this looks like a bug to me, would be great if you could open an issue on bitbucket and attach an example file together with options you used to run software. https://bitbucket.org/Davydov/godon/issues
Comments.UserDisplayName: Iakov Davydov
Tags: <phylogenetics><phylogeny><positive-selection><codon><godon>
Title: panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis
ThreadText: # panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis
  
  (Asked by: username_0 on 2020-10-12)
  
  I am using `godon` to find genes under positive selection with the **branch-site test**. However, after running for a little while I get the error *"panic: division of zero by zero or infinity by infinity"*.
  
  Below is the full output with the error report. I can supply the phylogenetic tree and fasta file I am using if that would be helpful. Thank you.
  
  > iter=33 lnL=-73104.072  
  > iter=66 lnL=-72956.855  
  > iter=99 lnL=-72912.956  
  > iter=131 lnL=-72902.900  
  > iter=162 lnL=-72900.147  
  > iter=194 lnL=-72898.562  
  > iter=226 lnL=-72897.970  
  > iter=258 lnL=-72897.651  
  > iter=289 lnL=-72897.435  
  > iter=321 lnL=-72897.284  
  > iter=353 lnL=-72897.199  
  > iter=385 lnL=-72897.153  
  > iter=416 lnL=-72897.108  
  > iter=448 lnL=-72897.076  
  > iter=17 lnL=-72890.551  
  > panic: division of zero by zero or infinity by infinity
  > goroutine 1 [running]:
  > math/big.(\*Float).Quo(0xc4273a8f40, 0xc4273a8f68, 0xc4273a8f18, 0xc42e88c118)
  > /usr/local/go/src/math/big/float.go:1639 +0x15c
  > bitbucket.org/username_1/godon/cmodel.(\*BranchSite).BEBPosterior(0xc422164120, 0xc4259bb900, 0x91, 0x91)
  > /go/src/bitbucket.org/username_1/godon/cmodel/bs.go:416 +0x6e9
  > bitbucket.org/username_1/godon/cmodel.(\*BranchSite).Final(0xc422164120, 0x101)
  > /go/src/bitbucket.org/username_1/godon/cmodel/bs.go:455 +0x112
  > main.computeFinal(0x1f263a0, 0xc422164120, 0xc4201522a0, 0x101, 0x6a80, 0x0)
  > /go/src/bitbucket.org/username_1/godon/godon/optimize.go:150 +0x93
  > main.performSingleTest(0xc420162320, 0xc428266000, 0x9399, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
  > /go/src/bitbucket.org/username_1/godon/godon/hyptest.go:335 +0x1b52
  > main.hypTest(0x1ee03a7, 0x1ee03a7, 0x4, 0xc4201aa501, 0x1, 0x1)
  > /go/src/bitbucket.org/username_1/godon/godon/hyptest.go:88 +0x71a
  > main.main()
  > /go/src/bitbucket.org/username_1/godon/godon/godon.go:316 +0xefa
  
  **Tags:** phylogenetics, phylogeny, positive-selection, codon, godon
  
  > **Comments:**
  > **username_1**: Hi, sorry about delay. Apparently I didn't subscribe properly to the tag.  Anyhow this looks like a bug to me, would be great if you could open an issue on bitbucket and attach an example file together with options you used to run software. https://bitbucket.org/username_1/godon/issues  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-10-12. Score: 1
  
  Ah wait you mentioned a branch sites test, right that makes sense. You've got two or more identical sequences in the analysis. Ensure there are no identical sequences in your alignments and ... PRESTO! It will work :-)
  
  Below are my original thoughts before I re-read your question. I've kept the notes because it helps explain the theory a bit. There is no need to supply the tree, it should be resolved.
  
  ---
  
  The tree likelihood looks to be decreasing nicely, so it can see both the tree and the codons in the alignment.
  
  At a guess the error relates to two or more indentical nucleotide sequences in your alignment. Thus zero non-synonymous sites (amino acid change) and zero synonymous (silent) sites. This error would only occur if you were calculating selection for each 'node' in the tree (internal branch). Alternatively, possibly if the number of synonymous sites was zero, regardless of the non-synonymous mutations this error could appear, but this doesn't seem to fit the error output.
  
  I don't know "Godon", but recommend `PAML` for this analysis. Admittedly it is complicated to deploy, but it is a very robust algorithm and hugely respected.
  
  
  ---
  
  