Dependencies and softwares

• Sequence visualization: AliView or a much simpler and faster option SeaView

• Sequence alignments: MAFFT

• Trimming alignment: trimAl

• Phylogenetic reconstruction:rapidNJ, RAxML, RAxML-ng, IQ-TREE, MrBayes and/or R (packages ape and phangorn)

• Tree visualization: figTree