Eric Coissac
8615da59a8
Introduces CLI flags for computing pairwise family overlap matrices and filtering genomes below a shared family threshold. Adds a free-loss mode that recodes locus non-detection states to missing data symbols in Sankoff-calibrated alignments, resolving ascertainment bias handling for IQ-TREE. Updates empirical transition parameters, removes the legacy model asset, and extends output writers for CSV diagnostics, FASTA pseudo-alignments, and Newick trees.
39 lines
565 B
Plaintext
39 lines
565 B
Plaintext
.venv/
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src/target
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data-stress
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*.fasta
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*.fasta.gz
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*.zst
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*.zst.meta
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*.pb
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./**/*.json
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*.bin
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*.log
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*.csv
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Betula_exilis--IGA-24-33
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benchmark/genomes
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benchmark/simulated_data
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benchmark/specimen_index_presence
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benchmark/specimen_index_count
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benchmark/global_index_presence
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benchmark/all_specific
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benchmark/global_index_count
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benchmark/stats
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benchmark/reference_index
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benchmark/reference_dist
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benchmark/obikmer_dist
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benchmark/specific_index_count
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benchmark/specific_index_presence
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TNT
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phyg
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*.tnt
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*.tre
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*.phy
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*.treefile
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*.bionj
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*.iqtree
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*.mldist
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*.parstree
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*.ckp.gz
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*.model
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