PAUP* error with exporting result file

Question

[ylkim9]

Hello, I want to ask about an error with my PAUP* (trial ver 4.0a169).

First, I followed the pipeline in here: https://github.com/mmatschiner/tutorials/blob/master/species_tree_inference_with_snp_data/README.md

Before the SVD quartet analysis, I called and filtered variants among 21 individuals (19 samples and 2 outgroups).

I changed this .vcf file into .nex file with the command:

  ruby convert_vcf_to_nexus.rb input.vcf input.nex

The result file looks like this:

#NEXUS

BEGIN DATA;
    DIMENSIONS NTAX=21 NCHAR=89911;
    FORMAT DATATYPE=DNA MISSING=N GAP=- 

MATRIX

CNHR_1       GCYAACTCGCWRGYMCRTGCRRYYMCYCACTC...
CNHR_2       GCYARYTCKCWGGYMCRTGCRRYYMCYCACTC...
CNGR_1       GYTAACTYGCWGGYMCRTGCRRYYMCYCACTC...
CNGR_2       GCTAACTYKCWGGYMCRTGCRRYYMCYCACTC...
CNMK_1       GCTAAYTCGCWGGYMCRTGCRRYYMCYCACTC...
CNMK_2       GCYAAYTCKCWGGYMCRTGCRRYYMCYCACTC...
CNYS_BH_1    KCTARYTCKCWGGYMCRTGCRRYYMCYCACTC...
CNYS_BH_2    GCTARYTCKCWGGYMCRTGMRRYYMCYCACTC...
CNYS_BH_3    GCYARYTCGCWGGCMMATGCRRYYMCYCMCTC...
CNYS_JS_1    KCTARYTCGCWGGYMCRTGCRRYYMCYCACTC...
CNYS_JS_2    GCYARCTCGCWGGYMCRTGCRRYYMCYCACTC...
CNYS_JS_3    KCYARCTCKCWGGYMCRTGCRRYYMCYCACTC...
CNYS_Y_1     KCTARCTCKCWGGCMCATGCRRYYMCYCACTC...
CNYS_Y_2     KCYARCTCGCWGGYMCRTGCRRYYMCYCACTC...
CNYS_Y_3     KCTARYTCKCWGGYMCRTGCRAYYMCYCACTC...
CNTJ_4       GCTRRYTCKCAGGCACATGCGRCTCCTMACTM...
CNTJ_5       GCTRRYTCGCAGGCACATGCGRCTCSTMACTM...
CTSJ_2       KCTARYTYKCAGGCMCATGMRRYYMSYMMCTC...
CTSJ_10      KYTARYTYKCAGGCMCATGCRRYYMSYMMCTC...
IL           GCTRRCTCGCAGGCMCRTGCGRCTCSTCACTC...
MM           GCTRRCTCGCAGGCACATGCGACTCSTCACTC...
;
END;

Then I also made partition file like this:

  BEGIN SETS;
TAXPARTITION SPECIES =
    CN_HR: 1-2,
    CN_GR: 3-4,
    CN_MK: 5-6,
    CN_YS_BH: 7-9,
    CN_YS_JS: 10-12,
    CN_YS_Y: 13-15,
    CN_TJ: 16-17,
    CT: 18-19,
    IL: 20,
    MM: 21;
  END;

Then I combined these .nex file and partition .txt file into a single .nex file with the command:

  cat input.nex taxpartitions.txt > input_wihtpartition.nex

Originally, I set both IL and MM as outgroups, but I only defined MM as outgroup in the Data menu in PAUP*. (I once had a wrong result with these taxa.) I set the SVD quartet options like the picture below:

The result printed in output display was like this: After the execution, I saved the result tree file with the option like the picture below:

However, when I opened the .tre file in figtree, the result was looked like this:

I set the input and output directory named in English, and didn't set the samples' name over 10 digits. I cannot find why my PAUP had a problem exporting the result file. Please anybody help me.

[Mark]

What is the issue with the figtree representation of the tree? i.e. what is missing?

I think you're trying to show partitions on the internal branches, if so you may need to select the variable in either node labels or branch labels