.venv/
.DS_Store
.claude/
.kilo/
.serena/
.zed/
.ast-cache/
CLAUDE.md
memory/
sandbox/
src/target
data-stress
*.fasta
*.fasta.gz
*.fastq
*.fastq.gz
*.vcf
*.zst
*.zst.meta
*.pb
**/*.json
*.bin
*.log
*.csv
*.meta
*.pfiv
*.done
*.efh
*.efl
*.bin.idx
*.prsb
Betula_exilis--IGA-24-33
benchmark/genomes
benchmark/genomes_orig
benchmark/simulated_data
benchmark/specimen_index_presence
benchmark/global_index_count_dense
benchmark/global_index_presence
benchmark/global_index_presence_orig
benchmark/global_index_presence_sav
benchmark/global_index_presence_dense
benchmark/all_specific
benchmark/global_index_count
benchmark/specimen_index_count
benchmark/stats
benchmark/reference_index
benchmark/reference_dist
benchmark/obikmer_dist
benchmark/specific_index_count
benchmark/specific_index_presence
benchmark/query_data
TNT
phyg
biblio
*.tnt
*.tre
*.phy
*.treefile
*.bionj
*.iqtree
*.mldist
*.parstree
*.ckp.gz
*.model