Request for Guidance on Mixed DNA and Binary Partition Analysis in IQ-TREE

[Russula1987]

My name is Aniket, and I am a researcher from India currently working with the IQ-TREE ver. 3 for phylogenetic analysis. I have encountered a problem while trying to perform a partitioned analysis that includes both DNA and binary data.

Specifically, I generated a binary matrix of ITS and LSU indels using FastGap. Afterward, I concatenated the ITS, LSU, and binary (indel) matrices using SeaView. I then attempted to analyze the combined dataset in IQ-TREE using the following partition file:

#nexus
begin sets;
DNA, ITS = 1-677;
DNA, LSU = 678-1592;
BINARY, INDELS = 1593-1725;
end;

My command was IQtree was: .\iqrtree3.exe -s Combined.fas -spp Partition.nex -m MFP+MERGE -bb 1000
However, IQ-TREE does not appear to recognize the binary matrix (encoded as 0 & 1 and, in case of Unknown, used "-"). I also tested the analysis using both PHYLIP and NEXUS file formats of the combined file, but the issue persists.