tool	role	version	key_parameters	source
DIAMOND	phylostratigraphy; all-vs-all clustering; SwissProt darkness	2.1.9	--ultra-sensitive; bitscore>=50; e-value<=1e-3	env/environment.yml
DENSE	synteny-based de novo emergence search	1.0.8	Nextflow pipeline; tBLASTn vs outgroup non-coding ORFs/UTRs	Roginski et al. 2024; Methods 4.3
HMMER3 (hmmscan)	Pfam-A domain annotation	3.4 (Aug 2023)	-E 1e-5; --domE 1e-5 (identical across cohorts)	env/environment.yml
PAML (codeml)	dN/dS (omega); site models	4.10	M0 single-omega; M1a/M2a; M7/M8; FDR-corrected LRTs	env/environment.yml
metapredict	intrinsic structural disorder	>=2.6	fraction residues with disorder score >= 0.5	env/environment.yml
AlphaFold3	3D structure prediction	v3.0.3 (open-source release, Docker image 8b274ec11b85, built 2026-06-18)	full-MSA monomer models; weights af3.bin (DeepMind; sha256 4638e384...); Python 3.12.3; 1x NVIDIA GB10 (DGX Spark), 20 cores, 121 GB RAM	Methods 4.6; code/README handover
FoldSeek	structural homology search	9.427df8a	easy-search; 3Di; target DB PDB100; E<1e-3	env/environment.yml
RepeatMasker	transposable-element / repeat screen	4.1.5	-species anopheles; TE-dominated defined as >=50% CDS covered	env/environment.yml
minimap2	local synteny anchoring (within DENSE)	(bundled with DENSE 1.0.8)	default	env/environment.yml
Nextflow	workflow engine	>=24.04.0	resourceLimits directive; -profile docker	nextflow.config
Weisman HDF model	homology-detection-failure flagging	Weisman et al. 2020	per-candidate detectability; flagged rather than discarded	Methods 4.2
jackhmmer (HMMER 3.4)	AF3 protein MSA generation	3.4 (Aug 2023)	UniRef90 2022_05; MGnify mgy_clusters 2022_05; small BFD (bfd-first_non_consensus_sequences); UniProt 2021_04 (paired MSA)	AF3 data pipeline
AF3 template search	structural templates	PDB seqres 2022_09_28	PDB mmCIF library (195,859 structures) via --pdb_database_path	AF3 data pipeline