Supplementary scripts for https://doi.org/10.1101/2025.10.03.680260

MASTER_commands_V2.sh - bash commands used for transcriptome assemblies, decontamination, protein prediction, OG inference and tree inference. Input files necessary to reproduce commands are available either via Figshare: https://doi.org/10.6084/m9.figshare.30214630 or, in case of raw reads, via NCBI records associated with Project PRJNA1332963.

Suppl_v2_scripts - R and Perl scripts used for visualisation and analysis of some MASTER_commands_V2.sh outputs. Please refer to the methods section in https://doi.org/10.1101/2025.10.03.680260 and/or comments of MASTER_commands_V2.sh outputs for notes on specific applications of each script.

source_tables_for_scripts.zip Tables used as inputs for blast_res_viz.Rmd and Orthofinder_stats_UNIVERSAL_V2.Rmd. If the input is absent, it can be produced from Figshare data using commands from MASTER_commands_V2.sh