How to input mixed morphological and protein data

[YanYan]

I follow the suggestion: each data type should be stored in a separate alignment file.

There are two file: Diplopoda10m.phy contains morphological data and Di90two.phy contains 90 gene amino acid.

Both of they have been input into IQ-tree to test. They are works. Diplopoda10m.phy need to add -st MORPH, Otherwise will be regarded as binary data by software.

I enter: bin\iqtree2 -s Diplopoda10m.phy -st MORPH –s Di90two.phy -st protein –p morph_aa_LG.nex -o Pauropus_h --date datednew.txt --date-tip 0

But it do not work

I attached to log and nex file here.

[Minh Bui]

Hi there,

This is not the valid command line, having two -s options, the second one will override the first one. Since you have already specified the alignment file names in the partition file, no need to use -s option. So the command line is something like:

bin\iqtree2 -p morph_aa_LG.nex -o Pauropus_h --date datednew.txt --date-tip 0

However, your partition file has “mv” for part1 model name, which is invalid. So something like:

#nexus

begin sets;

    charset part1 = Diplopoda10m.phy: *;

    charset part2 = Di90two.phy: *;

    charpartition mine = MK+G:part1, LG+C20+R4:part2;

end;

Or you can replace MK+G with the best-fit model for part1 (which can be done in a separate analysis).

Minh

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<morph_aa_LG.nex><morph_aa_LG.nex.log>

[YanYan]

Thank you very much！

I revised the nex file and the command as your suggestion.

It works! Sorry for so much mistake in my materials.

在 2020年7月9日星期四 UTC+8上午7:52:07，Minh Bui写道：

Hi there,

This is not the valid command line, having two -s options, the second one will override the first one. Since you have already specified the alignment file names in the partition file, no need to use -s option. So the command line is something like:

bin\iqtree2 -p morph_aa_LG.nex -o Pauropus_h --date datednew.txt --date-tip 0

However, your partition file has “mv” for part1 model name, which is invalid. So something like:

#nexus

begin sets;

    charset part1 = Diplopoda10m.phy: *;

    charset part2 = Di90two.phy: *;

    charpartition mine = MK+G:part1, LG+C20+R4:part2;

end;

Or you can replace MK+G with the best-fit model for part1 (which can be done in a separate analysis).

Minh

On 6 Jul 2020, at 2:19 pm, YanYan <lil...@163.com> wrote:

I follow the suggestion: each data type should be stored in a separate alignment file.

There are two file: Diplopoda10m.phy contains morphological data and Di90two.phy contains 90 gene amino acid.

Both of they have been input into IQ-tree to test. They are works. Diplopoda10m.phy need to add -st MORPH, Otherwise will be regarded as binary data by software.

I enter: bin\iqtree2 -s Diplopoda10m.phy -st MORPH –s Di90two.phy -st protein –p morph_aa_LG.nex -o Pauropus_h --date datednew.txt --date-tip 0

But it do not work

I attached to log and nex file here.

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