obikmer/benchmark/test_dist.csv at b77d8e9ca09cb9565e33be0789d6fd2fd7e79c35

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Eric Coissac 469e53b6f5 Add genomic distance benchmarking suite and test data

Introduces scripts to compute and validate pairwise genomic distance matrices across multiple metrics. Updates the Makefile with build and comparison targets, adds .gitignore rules for generated outputs, and includes test CSV matrices and a Newick phylogenetic tree for validating the distance computation pipeline.

2026-06-22 18:24:30 +02:00

4.7 KiB

Raw Blame History

1	genome	Candidozyma_auris--GCF_003013715.1_ASM301371v2	Acidobacterium_capsulatum--ATCC_51196	Bacillus_subtilis--168	Escherichia_coli--CFT073	Escherichia_coli--EDL933	Escherichia_coli--K-12_MG1655	Escherichia_coli--K-12_W3110	Klebsiella_pneumoniae--ATCC_13883	Klebsiella_pneumoniae--HS11286	Klebsiella_pneumoniae--MGH_78578	Opitutus_terrae--PB90-1	Proteus_mirabilis--HI4320	Saccharolobus_islandicus--M.16.4	Salmonella_enterica--AKU_12601	Salmonella_enterica--CT18	Salmonella_enterica--LT2	Salmonella_enterica--P125109	Shouchella_clausii--KSM-K16	Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1	Yersinia_ruckeri--YRB
2	Candidozyma_auris--GCF_003013715.1_ASM301371v2	0.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000
3	Acidobacterium_capsulatum--ATCC_51196	1.000000	0.000000	0.999981	0.999990	0.999989	0.999987	0.999987	0.999990	0.999988	0.999988	0.999994	0.999989	1.000000	0.999988	0.999987	0.999987	0.999988	0.999989	0.999991	0.999987
4	Bacillus_subtilis--168	1.000000	0.999981	0.000000	0.999990	0.999989	0.999989	0.999989	0.999989	0.999988	0.999986	0.999995	0.999985	0.999999	0.999988	0.999987	0.999989	0.999988	0.999778	0.999993	0.999987
5	Escherichia_coli--CFT073	1.000000	0.999990	0.999990	0.000000	0.825741	0.807495	0.807218	0.991156	0.996855	0.997849	0.999996	0.999633	1.000000	0.993885	0.996736	0.994148	0.993821	0.999991	0.999984	0.999291
6	Escherichia_coli--EDL933	1.000000	0.999989	0.999989	0.825741	0.000000	0.735107	0.734775	0.996126	0.998058	0.997908	0.999997	0.999640	1.000000	0.993993	0.997126	0.994390	0.994059	0.999991	0.999986	0.999292
7	Escherichia_coli--K-12_MG1655	1.000000	0.999987	0.999989	0.807495	0.735107	0.000000	0.382567	0.996190	0.997747	0.997455	0.999996	0.999604	1.000000	0.993444	0.996645	0.993773	0.993431	0.999989	0.999984	0.999174
8	Escherichia_coli--K-12_W3110	1.000000	0.999987	0.999989	0.807218	0.734775	0.382567	0.000000	0.996220	0.997761	0.997467	0.999995	0.999604	1.000000	0.993445	0.996669	0.993769	0.993443	0.999990	0.999985	0.999165
9	Klebsiella_pneumoniae--ATCC_13883	1.000000	0.999990	0.999989	0.991156	0.996126	0.996190	0.996220	0.000000	0.845220	0.840545	0.999997	0.999648	1.000000	0.996177	0.998128	0.996268	0.996052	0.999990	0.999987	0.999325
10	Klebsiella_pneumoniae--HS11286	1.000000	0.999988	0.999988	0.996855	0.998058	0.997747	0.997761	0.845220	0.000000	0.906475	0.999996	0.999683	1.000000	0.997724	0.995697	0.997776	0.997769	0.999989	0.999979	0.999463
11	Klebsiella_pneumoniae--MGH_78578	1.000000	0.999988	0.999986	0.997849	0.997908	0.997455	0.997467	0.840545	0.906475	0.000000	0.999996	0.999704	1.000000	0.997928	0.995054	0.997844	0.997868	0.999990	0.999980	0.999479
12	Opitutus_terrae--PB90-1	1.000000	0.999994	0.999995	0.999996	0.999997	0.999996	0.999995	0.999997	0.999996	0.999996	0.000000	0.999997	0.999998	0.999996	0.999996	0.999996	0.999995	0.999997	0.999993	0.999996
13	Proteus_mirabilis--HI4320	1.000000	0.999989	0.999985	0.999633	0.999640	0.999604	0.999604	0.999648	0.999683	0.999704	0.999997	0.000000	1.000000	0.999604	0.999699	0.999622	0.999613	0.999987	0.999983	0.999505
14	Saccharolobus_islandicus--M.16.4	1.000000	1.000000	0.999999	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	0.999998	1.000000	0.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000	1.000000
15	Salmonella_enterica--AKU_12601	1.000000	0.999988	0.999988	0.993885	0.993993	0.993444	0.993445	0.996177	0.997724	0.997928	0.999996	0.999604	1.000000	0.000000	0.869238	0.682277	0.663383	0.999990	0.999985	0.999260
16	Salmonella_enterica--CT18	1.000000	0.999987	0.999987	0.996736	0.997126	0.996645	0.996669	0.998128	0.995697	0.995054	0.999996	0.999699	1.000000	0.869238	0.000000	0.890872	0.886148	0.999988	0.999976	0.999524
17	Salmonella_enterica--LT2	1.000000	0.999987	0.999989	0.994148	0.994390	0.993773	0.993769	0.996268	0.997776	0.997844	0.999996	0.999622	1.000000	0.682277	0.890872	0.000000	0.622606	0.999989	0.999985	0.999296
18	Salmonella_enterica--P125109	1.000000	0.999988	0.999988	0.993821	0.994059	0.993431	0.993443	0.996052	0.997769	0.997868	0.999995	0.999613	1.000000	0.663383	0.886148	0.622606	0.000000	0.999988	0.999983	0.999270
19	Shouchella_clausii--KSM-K16	1.000000	0.999989	0.999778	0.999991	0.999991	0.999989	0.999990	0.999990	0.999989	0.999990	0.999997	0.999987	1.000000	0.999990	0.999988	0.999989	0.999988	0.000000	0.999991	0.999988
20	Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1	1.000000	0.999991	0.999993	0.999984	0.999986	0.999984	0.999985	0.999987	0.999979	0.999980	0.999993	0.999983	1.000000	0.999985	0.999976	0.999985	0.999983	0.999991	0.000000	0.999983
21	Yersinia_ruckeri--YRB	1.000000	0.999987	0.999987	0.999291	0.999292	0.999174	0.999165	0.999325	0.999463	0.999479	0.999996	0.999505	1.000000	0.999260	0.999524	0.999296	0.999270	0.999988	0.999983	0.000000

4.7 KiB Raw Blame History

4.7 KiB

Raw Blame History