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.
63 lines
1.0 KiB
Plaintext
63 lines
1.0 KiB
Plaintext
#nexus
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BEGIN Taxa;
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DIMENSIONS ntax=13;
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TAXLABELS
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[1] 'Escherichia_coli--CFT073'
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[2] 'Escherichia_coli--EDL933'
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[3] 'Escherichia_coli--K-12_MG1655'
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[4] 'Escherichia_coli--K-12_W3110'
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[5] 'Klebsiella_pneumoniae--ATCC_13883'
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[6] 'Klebsiella_pneumoniae--HS11286'
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[7] 'Klebsiella_pneumoniae--MGH_78578'
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[8] 'Proteus_mirabilis--HI4320'
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[9] 'Salmonella_enterica--AKU_12601'
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[10] 'Salmonella_enterica--CT18'
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[11] 'Salmonella_enterica--LT2'
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[12] 'Salmonella_enterica--P125109'
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[13] 'Yersinia_ruckeri--YRB'
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;
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END; [Taxa]
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BEGIN Splits;
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DIMENSIONS ntax=13 nsplits=34;
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FORMAT labels=no weights=yes confidences=no intervals=no;
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MATRIX
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100 2,
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100 3,
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100 4,
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100 3 4,
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69 2 3 4,
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100 5,
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100 7,
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16 5 7,
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100 6,
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100 13,
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16 6 13,
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23 5 6 7 13,
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100 8,
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100 10,
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23 8 10,
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100 9,
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100 11,
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100 12,
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100 11 12,
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100 9 11 12,
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23 8 9 10 11 12,
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100 1 2 3 4,
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100 1,
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84 7 13,
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83 5 7 13,
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77 6 8,
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76 5 6 7 8 13,
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76 9 10 11 12,
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31 1 2,
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1 5 6 7 8,
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1 10 13,
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1 9 10 11 12 13,
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1 5 6 13,
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1 5 6 8,
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;
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END; [Splits]
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