Skip to content
This repository was archived by the owner on Feb 6, 2024. It is now read-only.
This repository was archived by the owner on Feb 6, 2024. It is now read-only.

IQ-TREE Error: Range is not multiple of 3 #254

@fdegiglio

Description

@fdegiglio

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions