zhangrengang

F_ana_Camarosa_6-28-17.fasta.gz. But you may not get the identical results but similar results.

F_ana_Camarosa_6-28-17_unmasked.fasta.gz

Great. Thanks for your feedback.

@kashiff007 It seems that your genome is contig-level, but not chromosome-level?

@kashiff007 Can you show the homoelogous relationship such as dot plot, and your config file? How much percent do the largest 20 contigs account for the whole genome?

@kashiff007 It seems no problem. Do you have evidence for `allo`?

@kashiff007 If there are no much assembly errors (swtich errors, etc,), your genome is likely to be an auto-polyploid or be heavily recombined, which can not by phased by `subphaser`....

Yes, it is because preceding subgenome assignment is failed. Can you post the clustering heatmap?

@mrmrwinter The immediate cause should be that there is no subgenome-specific LTR for building tree. You can skip this step by `-disable_ltrtree`. And check the results according to the [Supplementary...

@mrmrwinter How about the plot `*.kmer.mat.pdf`? Your genome may be not a neoallopolyploid. Do you have a dot plot to show the homoeologs? By the way, you do not need...