obikmer

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Author	SHA1	Message	Date
Eric Coissac	19f4ec2567	Add documentation for whole-index distance metrics. Adds documentation describing metrics that operate directly on kmer sets or counts stored in an index, clarifying that they do not require per-locus SNP calling.	2026-09-12 17:56:37 +02:00
Eric Coissac	97fe82159a	Refactor Kmer indexing and add phylogenetic analysis features This commit introduces a complete overhaul of the Kmer indexing architecture, including new support for 2-bit encoding, canonical super-kmer handling, and a partitioned processing pipeline. Additionally, it adds comprehensive phylogenetic capabilities, including multiple distance metrics, SNP correction models, and models for rate heterogeneity and sampling design.	2026-09-12 17:45:11 +02:00

Author

SHA1

Message

Date

Eric Coissac

19f4ec2567

Add documentation for whole-index distance metrics.

Adds documentation describing metrics that operate directly on kmer sets or counts stored in an index, clarifying that they do not require per-locus SNP calling.

2026-09-12 17:56:37 +02:00

Eric Coissac

97fe82159a

Refactor Kmer indexing and add phylogenetic analysis features

This commit introduces a complete overhaul of the Kmer indexing architecture, including new support for 2-bit encoding, canonical super-kmer handling, and a partitioned processing pipeline. Additionally, it adds comprehensive phylogenetic capabilities, including multiple distance metrics, SNP correction models, and models for rate heterogeneity and sampling design.

2026-09-12 17:45:11 +02:00

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