# iqtree - concatenated
iqtree2 -s praomyini_concatenated_iqtree.phy -p praomyini_concatenated_iqtree_partitions.nex -m MFP+MERGE -B 1000 -T 8 --prefix prao_concat_iqtree

# iqtree - mtdna
iqtree2 -s praomyini_mtdna_iqtree.phy -p praomyini_mtdna_iqtree_partitions.nex -m MFP+MERGE -B 1000 -T 8 --prefix prao_mtdna_iqtree

# mrbayes - concatenated
mb praomyini_concatenated_mrbayes.nexus

# mrbayes - mtdna
mb praomyini_mtdna_mrbayes.nexus

# mrbayes - gene trees
files="./praomyini_genetrees_mrbayes/*.nexus"
for f in $files
do 
     mb "$f"
done

# ASTRAL
java -jar astral.5.7.5.jar -i praomyini_mrbayes_mbct_collapsed.nwk -o prao_astral_collapsed.tre

# fossilized birth-death dating (suppl.)
beast2 praomyini_divergence-dating-suppl.xml

# node calibration dating (main)
beast2 praomyini_divergence-dating-main.xml

