<p>Yes, it's easy.</p>
<pre><code>#nexus  
BEGIN SETS;

charset atp6.fasta = 1-651\3, 2-651\3;  
charset atp8.fasta = 652-729\3, 653-729\3;  
charset cob.fasta = 730-1749\3, 731-1749\3;  
# ... so on for every gene
END;
</code></pre>
<p>So for atp6 you will get 1,2,4,5,7,8,10,11 .... up to 651, and so on for each gene. Thus the residues at position 3, 6, 9, 12 are excluded.</p>

CC BY-SA 4.0
2023-12-19T09:02:23.863Z
Thank you very much, but by using the above charsets I get  "ERROR: Range 1-651\3, 2-651\3 is not multiple of 3 (necessary for codon data)". It's the same error that I get using other solutions suggested on the web; I don't understand why, using regular charsets without removing the third bases everything runs smoothly.
Francesco De Giglio
CC BY-SA 4.0
2023-12-12T17:15:39.790Z
2023-12-15T16:25:55.133Z
2023-12-15T16:25:55.133Z
M__
<p>I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets:</p>
<pre><code>nexus  
BEGIN SETS;

charset atp6.fasta = 1-651;  
charset atp8.fasta = 652-729;  
charset cob.fasta = 730-1749;  
charset cox1.fasta = 1750-3237;  
charset cox2.fasta = 3238-3858;  
charset cox3.fasta = 3859-4632;  
charset nad1.fasta = 4633-5484;  
charset nad2.fasta = 5485-6156;  
charset nad3.fasta = 6157-6459;  
charset nad4.fasta = 6460-7683;  
charset nad4L.fasta = 7684-7899;  
charset nad5.fasta = 7900-9294;  
charset nad6.fasta = 9295-9663;  
END;
</code></pre>
<p>I would need to remove the third bases, how should I write them? These are the commands with which I would launch IQ-TREE:</p>
<pre><code>iqtree -s &quot;fasta_file&quot; -bb 1000 -alrt 1000 -m MFP+MERGE -spp &quot;charset.nexus&quot; -st CODON5
</code></pre>
<p>Please, any suggestions would be very helpful.</p>

<phylogenetics><phylogeny><fasta><mtdna>
How to remove third codon positions from a charset in iqtree?
# How to remove third codon positions from a charset in iqtree?

(Asked by: username_0 on 2023-12-12)

I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets:
nexus  
BEGIN SETS;

charset atp6.fasta = 1-651;  
charset atp8.fasta = 652-729;  
charset cob.fasta = 730-1749;  
charset cox1.fasta = 1750-3237;  
charset cox2.fasta = 3238-3858;  
charset cox3.fasta = 3859-4632;  
charset nad1.fasta = 4633-5484;  
charset nad2.fasta = 5485-6156;  
charset nad3.fasta = 6157-6459;  
charset nad4.fasta = 6460-7683;  
charset nad4L.fasta = 7684-7899;  
charset nad5.fasta = 7900-9294;  
charset nad6.fasta = 9295-9663;  
END;

I would need to remove the third bases, how should I write them? These are the commands with which I would launch IQ-TREE:
iqtree -s "fasta_file" -bb 1000 -alrt 1000 -m MFP+MERGE -spp "charset.nexus" -st CODON5

Please, any suggestions would be very helpful.

**Tags:** phylogenetics, phylogeny, fasta, mtdna

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## 1 answers

### Answer by username_1 on 2023-12-12. Score: 0

Yes, it's easy.
#nexus  
BEGIN SETS;

charset atp6.fasta = 1-651\3, 2-651\3;  
charset atp8.fasta = 652-729\3, 653-729\3;  
charset cob.fasta = 730-1749\3, 731-1749\3;  
# ... so on for every gene
END;

So for atp6 you will get 1,2,4,5,7,8,10,11 .... up to 651, and so on for each gene. Thus the residues at position 3, 6, 9, 12 are excluded.

> **Comments:**
> **username_0**: Thank you very much, but by using the above charsets I get  "ERROR: Range 1-651\3, 2-651\3 is not multiple of 3 (necessary for codon data)". It's the same error that I get using other solutions suggested on the web; I don't understand why, using regular charsets without removing the third bases everything runs smoothly.  

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