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24 months ago
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Hey all!
I'm new to this forum so sorry if I do something wrong. I did a SNP analysis following these steps:
Snippy -> snippy-core -> snippy_clean_full_aln -> gubbins -> snp-sites -> IQTREE
The gubbins generated tree has a very nice topology but no branch support values so I went to check the generated tree with IQ-TREE
( iqtree -nt AUTO -fconst 32781,37052,37202,32295 -s norec_snp_clean -b 1000 )
and the trees are VERY different. My guts tell me I should trust the IQ-TREE but the gubbins tree tells a nicer story :)
Any opinions on this? Which tree should I keep?
