Error: Nexus file format

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RJ

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Jul 27, 2020, 4:50:19 AM7/27/20
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I am writing this email with regard to the error message that I am getting on the IQTREE web server while running the analysis.

ERROR: Partition file is not in NEXUS format, assuming RAxML-style partition file...
ERROR: Please specify alignment positions for partitionGTR+G:Subset2, GTR+G:Subset3, GTR+I:Subset4, GTR+G:Subset5, GTR+G:Subset6, GTR+G:Subset7;\
ERROR: end;\
ERROR: \ 
ERROR: }

Below is the alignment partitioning detail that I am using to run the analysis. 

#nexus
begin sets;
charset Subset1 = 1-519;
charset Subset2 = 520-1190;
charset Subset3 = 1191-1906\3;
charset Subset4 = 1192-1906\3;
charset Subset5 = 1193-1906\3;
charset Subset6 = 1907-2276\3;
charset Subset7 = 1908-2276\3 1909-2276\3;
charpartition PartitionFinder = GTR+G:Subset1, K80+G:Subset2, F81:Subset3, GTR+I:Subset4, HKY+G:Subset5, HKY:Subset6, JC:Subset7;
end;

Kindly help me.

Rob Lanfear

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Jul 27, 2020, 4:54:52 AM7/27/20
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Hi RJ,

This is a question for the IQ-TREE google group. It looks like PartitionFinder worked fine.

Rob

RJ

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Jul 27, 2020, 5:17:19 AM7/27/20
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Hi Rob,

Thanks for replying. I posted the error message on IQ-TREE group also, last Friday. But haven't received any reply. I am really stuck and need help.

Best
RJ
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