How to remove 3rd codon positions in a multiple sequence allignment?
0
0
Entering edit mode
11 weeks ago

Hello everyone. I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrates. 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.

iqtree CODON5 charset • 280 views
ADD COMMENT
0
Entering edit mode

What is the meaning of this i tag?

ADD REPLY

Login before adding your answer.

Traffic: 2016 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6