Eric Coissac 3da501349b docs: clarify phylogenetic output files and tool usage ...

Restructure the output files section into categorized subsections with tables. Add explicit mappings between command-line options and generated files. Define CSV matrix conventions, clarify mathematical formulas for distance calculations, and document execution commands for external phylogenetic tools.

2026-08-16 13:17:51 +02:00

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annotate.md

docs: add obikmer user guide and MkDocs build configuration

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dump.md

docs: add obikmer user guide and MkDocs build configuration

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estimate.md

docs: add obikmer user guide and MkDocs build configuration

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filter.md

docs: add obikmer user guide and MkDocs build configuration

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index_command.md

docs: add obikmer user guide and MkDocs build configuration

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merge.md

docs: add obikmer user guide and MkDocs build configuration

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name-tree.md

add name-tree command and fix --free-loss cost matrix

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pack.md

docs: add obikmer user guide and MkDocs build configuration

2026-08-13 17:19:01 +02:00

phylo.md

docs: clarify phylogenetic output files and tool usage

2026-08-16 13:17:51 +02:00

predicates.md

docs: add obikmer user guide and MkDocs build configuration

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query.md

docs: add obikmer user guide and MkDocs build configuration

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reindex.md

docs: add obikmer user guide and MkDocs build configuration

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select.md

docs: add obikmer user guide and MkDocs build configuration

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superkmer.md

docs: add obikmer user guide and MkDocs build configuration

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unitig.md

docs: add obikmer user guide and MkDocs build configuration

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utils.md

docs: add obikmer user guide and MkDocs build configuration

2026-08-13 17:19:01 +02:00