Phylogenetic analysis files for RNA viruses of parasitic nematodes.

Sequence alignment of the Brugia malayi RNA Virus 1 and Onchocerca volvulus RNA Virus 1 groups, using the "Hepe-Virga" and "Mono-Chu" clade alignments from Shi et al. 2016 as a base respectively. Both alignments were supplemented by sequences from Dheilly et al. 2022. The identified RdRP sequences from this study were then added to these alignments based on their putative virus orders. Additional RdRP sequences from viruses of flatworms that were more than 50% complete (less than 50% of identified amino acids were ‘X’) were also added for completeness, with all sequences re-aligned using MAFFT (v.7.505) using the E-INS-I strategy. Uninformative parts of the sequence were then removed using Trimal (v1.2rev59), with the gappyout strategy specified. The final alignment was then used for phylogenetic analysis using IQTree (v.1.6.1) at 1000 non-parametric bootstraps. ModelFinder was also used to identify the best evolutionary model for BMRV1 and OVRV1 (LG+F+I+G4 for all).The above method was also used to generate full phylogenetic trees for viruses identified as part of the Bunyavirales (best-determined evolutionary model LG+F+I+G4), Durnavirales (LG+F+G4), Flavivirus (LG+I+G4), Ghabrivirales (LG+G4), Jingchu-Monovirales (LG+F+I+G4), Martellivrales (LG+F+I+G4), Picornavirales (LG+F+I+G4), Qinviridae (LG+I+G4), and Reovirales (LG+F+I+G4) groups.The uploaded sequence alignments (fasta file format) are those used by IQTree to build the final phylogenetic tree. The newick-formatted treefiles for all aforementioned viruses are also available (nwk file format).