mix data with DNA sequences and binary data

Diego Zhu

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Jun 8, 2019, 5:40:20 AM6/8/19

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Hi,

I tried to code indel in my alignment as binary data. I would like to have iqtree infer the phylogenetic relationship using both the sequence and binary data. I wonder what is the input file looks like for this type of input data? Is it going to be sequence directly followed by the binary data e.g. atcgttg011101? Many thanks!

Kind Regards,

Diego

Diego Zhu

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Jun 11, 2019, 6:46:23 PM6/11/19

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Can anyone help me with this, please?

Minh Bui

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Jun 11, 2019, 9:52:09 PM6/11/19

to IQ-TREE, Diego Zhu

Hi Diego,

Sorry for the delay. You can’t mix DNA and binary in one alignment file. You need to prepare 2 files: the DNA alignment (also your original file; say dna.phy) and the binary alignment file (e.g. bin.phy). Then prepare this partition file:

#nexus

begin sets;

charset p1=dna.phy:*;

charset p2=bin.phy:*;

end;

You can now run IQ-TREE, where the basic command is:

iqtree -sp partition_file

For more details see the doc: http://www.iqtree.org/doc/Complex-Models#partition-models

Cheers,

Minh

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Diego Zhu

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Jun 12, 2019, 9:09:19 PM6/12/19

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Thank you very much Minh! I will have a go.

On Wednesday, 12 June 2019 11:52:09 UTC+10, Minh Bui wrote:

Hi Diego,

Sorry for the delay. You can’t mix DNA and binary in one alignment file. You need to prepare 2 files: the DNA alignment (also your original file; say dna.phy) and the binary alignment file (e.g. bin.phy). Then prepare this partition file:

#nexus
begin sets;
charset p1=dna.phy:*;
charset p2=bin.phy:*;
end;

You can now run IQ-TREE, where the basic command is:

iqtree -sp partition_file

For more details see the doc: http://www.iqtree.org/doc/Complex-Models#partition-models

Cheers,
Minh

On 12 Jun 2019, at 8:46 am, Diego Zhu <diegoz...@gmail.com> wrote:

Can anyone help me with this, please?

On Saturday, 8 June 2019 19:40:20 UTC+10, Diego Zhu wrote:
Hi,

I tried to code indel in my alignment as binary data. I would like to have iqtree infer the phylogenetic relationship using both the sequence and binary data. I wonder what is the input file looks like for this type of input data? Is it going to be sequence directly followed by the binary data e.g. atcgttg011101? Many thanks!

Kind Regards,

Diego

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