I am getting error for the Nexus file format while running analysis on IQTREE web-server.
I am working with four gene sequences comprising a sequence matrix of a total of 2276 nucleotides. I ran PartitionFinder on the total nucleotide sequence and used the partitioning scheme and substitution models details received by the software in NEXUS format to run ML analysis on IQTREE web server. IQTREE repeatedly giving me this following error!
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;\
Below is the alignment partitioning detail that I am using to run the analysis.
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;
Looking forward for help