Eric Coissac
55d7fa2067
Implements a calibrated 16-state Sankoff substitution cost matrix and CLI pipeline for evolutionary distance computation, including empirical calibration via saturation-filtered SNP counts. Refactors the sibling scanning stage to use batched transforms for improved synchronization efficiency. Introduces an OS-level advisory directory lock across all index-modifying commands to prevent concurrent write corruption. Updates dependencies and exposes new Sankoff utilities in the public API.
1 line
1.4 KiB
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1 line
1.4 KiB
Plaintext
(((((((((((((Salmonella_enterica--P125109:0.009029074806027838,Salmonella_enterica--LT2:0.010374535686866677):0.00299392644685007,Salmonella_enterica--AKU_12601:0.010129090864056669):0.008889984754373365,Salmonella_enterica--CT18:0.029563522158784489):0.05178212639099835,(Escherichia_coli--CFT073:0.018265758526676266,(Escherichia_coli--EDL933:0.01586939152374907,(Escherichia_coli--K-12_MG1655:0.0043321525684933419,Escherichia_coli--K-12_W3110:0.004373581717010194):0.007835004272817602):0.005522415854494232):0.05395833543383322):0.007199364670842333,(Klebsiella_pneumoniae--HS11286:0.027306681424389149,(Klebsiella_pneumoniae--ATCC_13883:0.015176538442299506,Klebsiella_pneumoniae--MGH_78578:0.026462018414958045):0.0015885400482290244):0.060738462006352359):0.029481404183583916,Yersinia_ruckeri--YRB:0.10269826524749153):0.004316815340436764,Proteus_mirabilis--HI4320:0.11745645944715785):0.04439101156727093,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1:0.17151356406519997):0.011344480816758762,Acidobacterium_capsulatum--ATCC_51196:0.17121217909071463):0.01869709592355495,Shouchella_clausii--KSM-K16:0.1554729916092201):0.04397682726757515,Bacillus_subtilis--168:0.10403127799132669):0.08828869671555731,Opitutus_terrae--PB90-1:0.06380512639846864):0.41655625366738377,Candidozyma_auris--GCF_003013715.1_ASM301371v2:0.22735026269091164,Saccharolobus_islandicus--M.16.4:0.21891918239548398); |