├── LICENSE ├── README.md ├── README.txt ├── bin ├── convert_gene_alignment_to_binary.sh ├── genapi ├── gene_db_alignment_against_seq.sh ├── generate_heatmap_all.R ├── generate_heatmap_missing.R ├── generate_heatmaps.R ├── phylogenetic_analysis.sh ├── remove_temp.sh └── settings.sh └── test_samples ├── E_coli ├── REL606.gff ├── SRR030253.gff ├── SRR030254.gff ├── SRR030255.gff ├── SRR030256.gff └── SRR030257.gff └── P_aeruginosa ├── PAO1_simulated_1.ffn ├── PAO1_simulated_2.ffn ├── PAO1_simulated_3.ffn ├── PAO1_simulated_4.ffn ├── PAO1_simulated_5.ffn ├── PAO1_simulated_6.ffn ├── PAO1_simulated_7.ffn └── PAO1_simulated_8.ffn /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/README.md -------------------------------------------------------------------------------- /README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/README.txt -------------------------------------------------------------------------------- /bin/convert_gene_alignment_to_binary.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/convert_gene_alignment_to_binary.sh -------------------------------------------------------------------------------- /bin/genapi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/genapi -------------------------------------------------------------------------------- /bin/gene_db_alignment_against_seq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/gene_db_alignment_against_seq.sh -------------------------------------------------------------------------------- /bin/generate_heatmap_all.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/generate_heatmap_all.R -------------------------------------------------------------------------------- /bin/generate_heatmap_missing.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/generate_heatmap_missing.R -------------------------------------------------------------------------------- /bin/generate_heatmaps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/generate_heatmaps.R -------------------------------------------------------------------------------- /bin/phylogenetic_analysis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/phylogenetic_analysis.sh -------------------------------------------------------------------------------- /bin/remove_temp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/remove_temp.sh -------------------------------------------------------------------------------- /bin/settings.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/bin/settings.sh -------------------------------------------------------------------------------- /test_samples/E_coli/REL606.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/E_coli/REL606.gff -------------------------------------------------------------------------------- /test_samples/E_coli/SRR030253.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/E_coli/SRR030253.gff -------------------------------------------------------------------------------- /test_samples/E_coli/SRR030254.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/E_coli/SRR030254.gff -------------------------------------------------------------------------------- /test_samples/E_coli/SRR030255.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/E_coli/SRR030255.gff -------------------------------------------------------------------------------- /test_samples/E_coli/SRR030256.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/E_coli/SRR030256.gff -------------------------------------------------------------------------------- /test_samples/E_coli/SRR030257.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/E_coli/SRR030257.gff -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_1.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_1.ffn -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_2.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_2.ffn -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_3.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_3.ffn -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_4.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_4.ffn -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_5.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_5.ffn -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_6.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_6.ffn -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_7.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_7.ffn -------------------------------------------------------------------------------- /test_samples/P_aeruginosa/PAO1_simulated_8.ffn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MigleSur/GenAPI/HEAD/test_samples/P_aeruginosa/PAO1_simulated_8.ffn --------------------------------------------------------------------------------