Eric Coissac
eee71430a4
Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
2 lines
712 B
Plaintext
2 lines
712 B
Plaintext
(Escherichia_coli--CFT073:0.7973338454,(Escherichia_coli--EDL933:0.5132866305,(Escherichia_coli--K-12_MG1655:0.2990687226,Escherichia_coli--K-12_W3110:0.3006288477)100:0.1655629834)69:0.0000007189,(((Klebsiella_pneumoniae--ATCC_13883:0.9661675519,(Klebsiella_pneumoniae--MGH_78578:0.3148953385,Yersinia_ruckeri--YRB:0.3576917943)84:0.4568464394)83:0.0727808943,(Klebsiella_pneumoniae--HS11286:0.1397401144,Proteus_mirabilis--HI4320:0.2192824480)77:0.3686486712)76:0.1162295711,((Salmonella_enterica--AKU_12601:0.6158730439,(Salmonella_enterica--LT2:0.4371443730,Salmonella_enterica--P125109:0.5815549929)100:0.1012287522)100:0.0714169372,Salmonella_enterica--CT18:0.2058143021)76:0.3641489914)100:0.2900565429);
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