Differences between Roginski et al. (2024) and Grandchamp et al. (2023):

DeNovoGeneAnnotation:

	inputData:

		values in Roginski et al. (2024) but not in Grandchamp et al. (2023):
		annotated genome

		values in Grandchamp et al. (2023) but not in Roginski et al. (2024):
		transcriptome

	inputAnnotGenome:

		values in Roginski et al. (2024) but not in Grandchamp et al. (2023):
		annotGenomeChoice: homology-based approach

	inputTranscriptome:

		values in Grandchamp et al. (2023) but not in Roginski et al. (2024):
		expressionLevel: 0.5
		transContextChoice: 
			intergenic
			antisense
			intronic
			overlap gene
		transORFChoice: longest ORF

	evolutionaryInformation:

		selection:

			differing values in Roginski et al. (2024) and Grandchamp et al. (2023):
			codeml
			dN/dS

	phylogeneticTaxa:

		taxSpecificity:

			differing values in Roginski et al. (2024) and Grandchamp et al. (2023):
			lineage-specific
			species-specific

		taxonID:

			taxID:

				differing values in Roginski et al. (2024) and Grandchamp et al. (2023):
				Drosophila melanogaster-drosophila
				7227

	homologyFilter:

		threshold:

			differing values in Roginski et al. (2024) and Grandchamp et al. (2023):
			e-value
			0.0001, 0.1

		dataBase:

			values in Roginski et al. (2024) but not in Grandchamp et al. (2023):
			NCBI NR

			values in Grandchamp et al. (2023) but not in Roginski et al. (2024):
			custom choice

		customDB:

			values in Grandchamp et al. (2023) but not in Roginski et al. (2024):
			Drosophila proteomes
			Dipteran proteomes

	nonCodingHomologs:

		enablingMutations:

			values in Grandchamp et al. (2023) but not in Roginski et al. (2024):
			True

		synteny:

			softwareSyntenySearch:

				values in Roginski et al. (2024) but not in Grandchamp et al. (2023):
				DENSE

			studyURL:

				values in Roginski et al. (2024) but not in Grandchamp et al. (2023):
				https://doi.org/10.1093/gbe/evae159

				values in Grandchamp et al. (2023) but not in Roginski et al. (2024):
				https://doi.org/10.1101/gr.277482.122