error to get phylogeny tree using LTR_tree.R script

[Ravindra-Raut]

Dear zhangrengang

I was using LTR_tree.R script, for getting phylogenetic tree from output files after running iqtree. I encounter the following error: Error in FUN(X[[i]], ...) : object 'Clade' not found

I am sharing both mapfile and treefile. Please check it and give the suggest.

[zhangrengang]

Hi, I cannot access your shared files. Please share the files via GitHub directly.

[zhangrengang]

Sorry, I cannot access google.

[Ravindra-Raut]

https://github.com/Ravindra-Raut/mapfile-and-treefiles

[zhangrengang]

Which version of iqtree do you use?

[zhangrengang]

It is because iqtree2 has changed its rule to convert special characters. I have fix it. Please try again.

[Ravindra-Raut]

I used iqtree2 version

[zhangrengang]

However, if you use concatenate_domains.py to generate alignments, all special characters will be converted to _.

[Ravindra-Raut]

Thank you for the help and appreciate your time and efforts.

[Ravindra-Raut]

O_sativa_A123_output_e.gydb.cls.tsv https://drive.google.com/file/d/1kZ37st8BrpFmo_uqNDbCx4RjIhZuFHGD/view?usp=drive_web O_sativa_A123_gydb_RT_output_f.treefile https://drive.google.com/file/d/1CT-CuJODa60mhteSjwA6xPT6_bEC-4sp/view?usp=drive_web

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On Thu, Jul 14, 2022 at 12:05 AM ravindra raut @.***> wrote:

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On Thu, Jul 14, 2022 at 12:01 AM Ravindra Raut @.***> wrote:

Dear zhangrengang

I was using LTR_tree.R script, for getting phylogenetic tree from output files after running iqtree. I encounter the following error: Error in FUN(X[[i]], ...) : object 'Clade' not found

I am sharing both mapfile and treefile. Please check it and give the suggest.

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