LICENSE
README.md
pyproject.toml
setup.py
gplace/__init__.py
gplace/__main__.py
gplace/cli.py
gplace/exceptions.py
gplace/fileio.py
gplace/main.py
gplace/biolib_lite/__init__.py
gplace/biolib_lite/common.py
gplace/biolib_lite/custom_help_formatter.py
gplace/biolib_lite/exceptions.py
gplace/biolib_lite/logger.py
gplace/config/__init__.py
gplace/config/common.py
gplace/config/output.py
gplace/engine/__init__.py
gplace/engine/build.py
gplace/engine/core.py
gplace/engine/factory.py
gplace/engine/fitted.py
gplace/engine/gamma.py
gplace/engine/iqtree.py
gplace/engine/jplace.py
gplace/engine/models.py
gplace/engine/newick.py
gplace/engine/placer.py
gplace/engine/raxmlng.py
gplace/engine/reference.py
gplace/engine/resources.py
gplace/engine/selftest.py
gplace/engine/stats.py
gplace/engine/taxonomy.py
gplace/engine/testsets.py
gplace/engine/tiled.py
gplace/engine/yang_gamma.py
gplace/engine/csrc/libm_bind.c
gplace/engine/csrc/xp.c
gplace/engine/csrc/core-math/LICENSE
gplace/engine/csrc/core-math/VERSION
gplace/engine/csrc/core-math/dint.h
gplace/engine/csrc/core-math/exp.c
gplace/engine/csrc/core-math/log.c
gplace/engine/csrc/core-math/sin.c
gplace/engine/csrc/core-math/pow/dint.h
gplace/engine/csrc/core-math/pow/pow.c
gplace/engine/csrc/core-math/pow/pow.h
gplace/engine/csrc/core-math/pow/qint.h
gplace/engine/csrc/glibc/README
gplace/engine/csrc/glibc/e_hypot.c
gplace/engine/csrc/glibc/math_private.h
gplace/engine/csrc/glibc/s_log1p.c
gplace/engine/data/iqtree_protein_models.json
gplace/engine/data/jtt.txt
gplace/engine/data/lg.txt
gplace/engine/data/raxmlng_protein_models.json
gplace/engine/data/stock_libm_vectors.tsv
gplace/engine/data/stock_wag_eigen.txt
gplace/engine/data/wag.txt
gplace/tests/data/expected_pplacer.jplace
gplace/tests/data/queries.fasta
gplace/tests/data/fits/README.md
gplace/tests/data/fits/full_dna_HKY_F_I_R2.ckp.gz
gplace/tests/data/fits/full_dna_HKY_F_I_R2.iqtree
gplace/tests/data/fits/full_dna_HKY_F_I_R2.treefile
gplace/tests/data/fits/full_mix_EX2.ckp.gz
gplace/tests/data/fits/full_mix_EX2.iqtree
gplace/tests/data/fits/full_mix_EX2.treefile
gplace/tests/data/fits/full_mix_LG4X.ckp.gz
gplace/tests/data/fits/full_mix_LG4X.iqtree
gplace/tests/data/fits/full_mix_LG4X.treefile
gplace/tests/data/fits/full_model_expected.json
gplace/tests/data/fits/full_partitioned_dna.ckp.gz
gplace/tests/data/fits/full_partitioned_dna.iqtree
gplace/tests/data/fits/full_prot_LG_G4_median.ckp.gz
gplace/tests/data/fits/full_prot_LG_G4_median.iqtree
gplace/tests/data/fits/full_prot_LG_G4_median.treefile
gplace/tests/data/fits/full_prot_Q_pfam_G4.ckp.gz
gplace/tests/data/fits/full_prot_Q_pfam_G4.iqtree
gplace/tests/data/fits/full_prot_Q_pfam_G4.treefile
gplace/tests/data/fits/iq_dna_HKY_F_G4.iqtree
gplace/tests/data/fits/iq_prot_LG.iqtree
gplace/tests/data/fits/iq_prot_LG_F_G4.iqtree
gplace/tests/data/fits/iq_prot_LG_F_G4.pplacer.jplace
gplace/tests/data/fits/iq_prot_LG_F_G4.treefile
gplace/tests/data/fits/iq_prot_LG_I_G4.iqtree
gplace/tests/data/fits/iq_prot_LG_R4.iqtree
gplace/tests/data/fits/iq_prot_Q_pfam_G4.iqtree
gplace/tests/data/fits/rx_dna_GTR_G4.pplacer.jplace
gplace/tests/data/fits/rx_dna_GTR_G4.raxml.bestTree
gplace/tests/data/fits/rx_dna_GTR_G4.raxml.log
gplace/tests/data/fits/rx_full_dna_GTR_I_R3.raxml.bestModel
gplace/tests/data/fits/rx_full_dna_GTR_I_R3.raxml.bestTree
gplace/tests/data/fits/rx_full_dna_GTR_I_R3.raxml.log
gplace/tests/data/fits/rx_full_dna_HKY_FC_I_G4.raxml.bestModel
gplace/tests/data/fits/rx_full_dna_HKY_FC_I_G4.raxml.bestTree
gplace/tests/data/fits/rx_full_dna_HKY_FC_I_G4.raxml.log
gplace/tests/data/fits/rx_full_expected.json
gplace/tests/data/fits/rx_full_prot_LG4X.raxml.bestModel
gplace/tests/data/fits/rx_full_prot_LG4X.raxml.bestTree
gplace/tests/data/fits/rx_full_prot_LG4X.raxml.log
gplace/tests/data/fits/rx_full_prot_LG_G4a.raxml.bestModel
gplace/tests/data/fits/rx_full_prot_LG_G4a.raxml.bestTree
gplace/tests/data/fits/rx_full_prot_LG_G4a.raxml.log
gplace/tests/data/fits/rx_full_prot_WAG_FC_IC_G4.raxml.bestModel
gplace/tests/data/fits/rx_full_prot_WAG_FC_IC_G4.raxml.bestTree
gplace/tests/data/fits/rx_full_prot_WAG_FC_IC_G4.raxml.log
gplace/tests/data/fits/rx_prot_LG_G4_FC.raxml.log
gplace/tests/data/fits/rx_prot_LG_G4_FO.raxml.log
gplace/tests/data/mini.refpkg/CONTENTS.json
gplace/tests/data/mini.refpkg/mini_msa.fa
gplace/tests/data/mini.refpkg/mini_tree.tree
gplace/tests/data/mini.refpkg/phylo_model.json
gplace/tests/data/models/README.md
gplace/tests/data/models/dna_cat.pplacer.jplace
gplace/tests/data/models/like_gtr.pplacer.jplace
gplace/tests/data/models/like_gtr_queries.fasta
gplace/tests/data/models/like_wag.pplacer.jplace
gplace/tests/data/models/like_wag_queries.fasta
gplace/tests/data/models/mini_JTT.phylo_model.json
gplace/tests/data/models/mini_JTT.pplacer.jplace
gplace/tests/data/models/mini_JTT_g0.7x8.phylo_model.json
gplace/tests/data/models/mini_JTT_g0.7x8.pplacer.jplace
gplace/tests/data/models/mini_JTT_g2.0x21.phylo_model.json
gplace/tests/data/models/mini_JTT_g2.0x21.pplacer.jplace
gplace/tests/data/models/mini_LG.phylo_model.json
gplace/tests/data/models/mini_LG.pplacer.jplace
gplace/tests/data/models/mini_LG_emp_g1.3x4.phylo_model.json
gplace/tests/data/models/mini_LG_emp_g1.3x4.pplacer.jplace
gplace/tests/data/models/mini_LG_g0.3x32.phylo_model.json
gplace/tests/data/models/mini_LG_g0.3x32.pplacer.jplace
gplace/tests/data/models/mini_WAG_emp.phylo_model.json
gplace/tests/data/models/mini_WAG_emp.pplacer.jplace
gplace/tests/data/models/mini_WAG_g0.05x4.fix.jplace
gplace/tests/data/models/mini_WAG_g0.05x4.phylo_model.json
gplace/tests/data/models/mini_WAG_g0.05x4.pplacer.jplace
gplace/tests/data/models/mini_WAG_g0.5x4.phylo_model.json
gplace/tests/data/models/mini_WAG_g0.5x4.pplacer.jplace
gplace/tests/data/models/mini_WAG_g0.6x24.phylo_model.json
gplace/tests/data/models/mini_WAG_g0.6x24.pplacer.jplace
gplace/tests/data/models/dna_cat.refpkg/CONTENTS.json
gplace/tests/data/models/dna_cat.refpkg/aln.fasta
gplace/tests/data/models/dna_cat.refpkg/phylo_model.json
gplace/tests/data/models/dna_cat.refpkg/tree.nwk
gplace/tests/data/models/like_gtr.refpkg/CONTENTS.json
gplace/tests/data/models/like_gtr.refpkg/aln.fasta
gplace/tests/data/models/like_gtr.refpkg/phylo_model.json
gplace/tests/data/models/like_gtr.refpkg/tree.nwk
gplace/tests/data/models/like_wag.refpkg/CONTENTS.json
gplace/tests/data/models/like_wag.refpkg/aln.fasta
gplace/tests/data/models/like_wag.refpkg/phylo_model.json
gplace/tests/data/models/like_wag.refpkg/tree.nwk
gplace/tests/data/options/RAxML8_info.gtr
gplace/tests/data/options/RAxML_info.gtr_fe
gplace/tests/data/options/RAxML_info.wag723
gplace/tests/data/options/README.md
gplace/tests/data/options/actin.fasta
gplace/tests/data/options/actin.phy_phyml_tree.txt
gplace/tests/data/options/actin_model.json
gplace/tests/data/options/always_refine_dna_cat.pplacer.jplace
gplace/tests/data/options/always_refine_mini.pplacer.jplace
gplace/tests/data/options/dna_cat.kf0.pplacer.jplace
gplace/tests/data/options/gtr_g.ms0.pplacer.jplace
gplace/tests/data/options/hiv.fasta
gplace/tests/data/options/hiv.phy_phyml_stats.txt
gplace/tests/data/options/hiv.phy_phyml_tree.txt
gplace/tests/data/options/json_wag_modelfreqs.pplacer.jplace
gplace/tests/data/options/mini.combo.pplacer.jplace
gplace/tests/data/options/mini.npm_dups.pplacer.jplace
gplace/tests/data/options/mini.p_like.pplacer.jplace
gplace/tests/data/options/nogamma_stats.txt
gplace/tests/data/options/phyml33_stats.txt
gplace/tests/data/options/phyml_gtr.pplacer.jplace
gplace/tests/data/options/phyml_nogamma_g.pplacer.jplace
gplace/tests/data/options/raxml_gtr_fe.pplacer.jplace
gplace/tests/data/options/raxml_wag.pplacer.jplace
gplace/tests/data/options/refine_mini_refs.pplacer.jplace
gplace/tests/data/options/refpkg_aln_sto.pplacer.jplace
gplace/tests/data/options/refs_in_query_no_r.pplacer.jplace
gplace/tests/data/options/wag_g.kam1.pplacer.jplace
gplace/tests/data/parity/mini_discard.pplacer.jplace
gplace/tests/data/parity/mini_full.seq_info.csv
gplace/tests/data/parity/mini_full.taxonomy.csv
gplace/tests/data/parity/mini_full_dups.pplacer.jplace
gplace/tests/data/parity/mini_full_dups_mrca.pplacer.jplace
gplace/tests/data/parity/mini_genus.seq_info.csv
gplace/tests/data/parity/mini_genus.taxonomy.csv
gplace/tests/data/parity/mini_genus_dups_mrca.pplacer.jplace
gplace/tests/data/parity/mini_partial.seq_info.csv
gplace/tests/data/parity/mini_partial.taxonomy.csv
gplace/tests/data/parity/mini_partial_dups.pplacer.jplace
gplace/tests/data/parity/mini_queries_dups.fasta
gplace/tests/data/parity/mini_queries_nonoverlap.fasta
gplace/tests/data/tools/dups.jplace
gplace/tests/data/tools/dups.tog.tre
gplace/tests/data/tools/dups.tog.xml
gplace/tests/data/tools/dups.tog_nn.tre
gplace/tests/data/tools/edge_cases.jplace
gplace/tests/data/tools/edge_cases.tog.tre
gplace/tests/data/tools/edge_cases.tog.xml
gplace/tests/data/tools/edge_cases.tog_nn.tre
gplace/tests/data/tools/expected_phylo_models.json
gplace/tests/data/tools/floatlabels.jplace
gplace/tests/data/tools/floatlabels.tog.tre
gplace/tests/data/tools/floatlabels.tog.xml
gplace/tests/data/tools/floatlabels.tog_nn.tre
gplace/tests/data/tools/names.jplace
gplace/tests/data/tools/names.tog.tre
gplace/tests/data/tools/names.tog.xml
gplace/tests/data/tools/names.tog_nn.tre
gplace/tests/data/tools/records.jplace
gplace/tests/data/tools/records.tog.tre
gplace/tests/data/tools/records.tog.xml
gplace/tests/data/tools/records.tog_nn.tre
gplace/tests/data/tools/stats_RAxML_info.gtr
gplace/tests/data/tools/stats_RAxML_info.lgf
gplace/tests/data/tools/stats_RAxML_info.wag
gplace/tests/data/tools/stats_ft_gtr.log
gplace/tests/data/tools/stats_ft_jtt.log
gplace/tests/data/tools/stats_ft_lg.log
gplace/tests/data/tools/stats_ft_wag.log
gplace/tests/data/tools/stats_iq_gtr.iqtree
gplace/tests/data/tools/stats_iq_lg.iqtree
gplace/tests/data/tools/stats_iq_wagf.iqtree
gplace/tests/data/tools/stats_pm_aa_e.phy_phyml_stats.txt
gplace/tests/data/tools/stats_pm_aa_m.phy_phyml_stats.txt
gplace/tests/data/tools/stats_pm_nt.phy_phyml_stats.txt
gplace/tests/data/tools/stats_rng_gtr.raxml.log
gplace/tests/data/tools/stats_rng_lg.raxml.log
gplace/tests/data/tools/stats_rng_wag.raxml.log
gplace/tools/__init__.py
gplace/tools/taxit.py
gplace/tools/tog.py
gtdb_gplace.egg-info/PKG-INFO
gtdb_gplace.egg-info/SOURCES.txt
gtdb_gplace.egg-info/dependency_links.txt
gtdb_gplace.egg-info/entry_points.txt
gtdb_gplace.egg-info/requires.txt
gtdb_gplace.egg-info/top_level.txt
tests/test_cli.py
tests/test_engine.py
tests/test_fitted.py
tests/test_full_model.py
tests/test_jplace.py
tests/test_models.py
tests/test_newick.py
tests/test_options.py
tests/test_parity.py
tests/test_resources.py
tests/test_tiled.py
tests/test_tools.py