REFERENCE TREE:
module load raxml-ng

raxml-ng --model GTR+G --threads 12  --seed 2 --tree pars{30},rand{30} --msa /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/allPelagos_Alignment_noCladeB4.phy --prefix reference_tree --redo --force


FOR PLACEMENT:


# Creates an aligqnment from the short sequences combined to the reference tree

module load papara

papara -j 5 -r -t /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/raxml_ng/reference_tree.raxml.bestTree -s /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/allPelagos_Alignment_noCladeB4.phy -q /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/ASVs_V4_selectionTREE.fasta



module load epa-ng/0.3.8

#we need to split the papara output to only get the queries (output file: query.fasta)
#epa-ng --split /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/allPelagos_Alignment_noCladeB4.phy papara_alignment.default

#Now we do the REAL placement (remember that the reference aligment with the long sequences should be a fasta file in this program)
epa-ng --redo -t /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/raxml_ng/reference_tree.raxml.bestTree -s allPelagos_Alignment_noCladeB4.fasta -q query.fasta -w ./ --model /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/raxml_ng/reference_tree.raxml.bestModel