Warning message when adding morphology partition via Philip format

[Matthew Green]

Hey Folks,

Received the below warning message when loading the morphology partition (35 characters, "0 1" states) of a mixed data (DNA+morphology) nex partition file. 

Reading alignment file Pycnopsyche_Adult_Morphology.phy ... Phylip format detected

Alignment most likely contains binary sequences

WARNING: Your specified sequence type is different from the detected one

Alignment has 184 sequences with 35 columns, 32 distinct patterns

33 parsimony-informative, 2 singleton sites, 0 constant sites

IQ-Tree seems to be running fine currently and is going through bootstrap iterations, but I'm wondering if anyone else has had this issue.

Here's the command and partition file:

-p Pycnopsyche_Adults_Larvae_Adult_Morphology_Partition_Sets.nex -m TESTMERGE -b 1000 -T AUTO 

#NEXUS 

BEGIN SETS;

    CHARSET CO1 = Pycnopsyche_CO1_CAD.phy: DNA,1-658;

    CHARSET CAD = Pycnopsyche_CO1_CAD.phy: DNA,659-1416;

    CHARSET Adult_Morphology = Pycnopsyche_Adult_Morphology.phy: MORPH,1-35;

END;

Linked .phy files in the partition were converted from .nex to .phy in mesquite. I initially had problems with IQ-Tree finding MK models when using nexus files. I converted the .nex files to .phy and this problem went away. Believe it or not, the TESTMERGE command will find an appropriate MK model via partition finder, so I did not specify a model for each partition in partition file. 

However, I'm wondering if folks have received the above error message and how they have fixed the issue.

All the best,

Matt Green.

[Minh Bui]

Hi Matt,

It’s a warning, not an error. Normally, if you have 0-1 states, it will be detected as BIN (for binary data). So the warning will be gone if you change “MORPH” in partition file to “BIN”. 

However, since morphological data generalise binary data, it will work just fine. The only difference will be in the model names, (JC2 and GTR2 for binary, whereas MK and ORDERED for morphological data). So I don’t see any problem here.

Cheers

Minh

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[Matthew Green]

Hey Minh,

Thanks for letting me know. After I sent this message, I did think that I received the warning message because I told IQ-Tree to expect morphological data.

Thanks!

Matt.