Gabriel Renaud
Gabriel Renaud
same as jelissa03
sorry yes you are right but I still get the same error.
ok I am actually trying to generate a new tree where I substitute entire subtrees for a single leaf, is this possible? It was complaining that my tree was not...
and the -rootbyoutgroup has worked.
A few things: 1) did you trim adapters/merge the paired-end data? 2) I recommend mapping with bwa aln with parameters: -n 0.01 -o 2 -l 16500. 3) did you map...
Ok do you have any signs of aDNA damage on the mitogenome?
How many fragments did you end up mapping?
yes please, via email.
can you please open a new issue, post all the commands you have used and potentially send them to me via email?
schmutzi handles damage internally and this is what powers the inference. You do not need to trim anything just map your ancient DNA fragments to the mitochondrial genome in isolation