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This repository has been archived by the owner on Feb 6, 2024. It is now read-only.
Good morning. 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;
Good morning. 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;
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
Using the charsets above, everything okay. Now I would like to remove the third bases. I tried to modify my charsets in this way:
#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;
charset cox1.fasta = 1750-3237\3, 1751-3237\3;
charset cox2.fasta = 3238-3858\3, 3239-3858\3;
charset cox3.fasta = 3859-4632\3, 3860-4632\3;
charset nad1.fasta = 4633-5484\3, 4634-5484\3;
charset nad2.fasta = 5485-6156\3, 5486-6156\3;
charset nad3.fasta = 6157-6459\3, 6158-6459\3;
charset nad4.fasta = 6460-7683\3, 6461-7683\3;
charset nad4L.fasta = 7684-7899\3, 7685-7899\3;
charset nad5.fasta = 7900-9294\3, 7901-9294\3;
charset nad6.fasta = 9295-9663\3, 9296-9663\3;
END;
What I get is "ERROR: Range 1-651\3, 2-651\3 is not multiple of 3 (necessary for codon data)".
Please, any suggestions would be very helpful.
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