LICENSE
MANIFEST.in
README.md
pyproject.toml
FunVIP.egg-info/PKG-INFO
FunVIP.egg-info/SOURCES.txt
FunVIP.egg-info/dependency_links.txt
FunVIP.egg-info/entry_points.txt
FunVIP.egg-info/requires.txt
FunVIP.egg-info/top_level.txt
funvip/FunVIP_GUI.py
funvip/__init__.py
funvip/main.py
funvip/_vendor/__init__.py
funvip/_vendor/ete4_wheels/LICENSE
funvip/_vendor/ete4_wheels/README.md
funvip/_vendor/ete4_wheels/ete4-4.4.0-cp312-cp312-win_amd64.whl
funvip/data/Option_manager.xlsx
funvip/data/__init__.py
funvip/data/genus_line.txt
funvip/external/MAFFT_LICENSE
funvip/external/MAFFT_Windows.zip
funvip/external/__init__.py
funvip/external/BLAST_Windows/Uninstall-ncbi-blast-2.12.0+.exe
funvip/external/BLAST_Windows/bin/blastn.exe
funvip/external/BLAST_Windows/bin/cleanup-blastdb-volumes.py
funvip/external/BLAST_Windows/bin/get_species_taxids.sh
funvip/external/BLAST_Windows/bin/legacy_blast.pl
funvip/external/BLAST_Windows/bin/makeblastdb.exe
funvip/external/BLAST_Windows/bin/nghttp2.dll
funvip/external/BLAST_Windows/bin/update_blastdb.pl
funvip/external/BLAST_Windows/doc/README.txt
funvip/external/FastTree_Windows/FastTree.exe
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Gblocks.exe
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/nad3.pir
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/paths
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Documentation/Gblocks_documentation.html
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cox2.pir
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cytb.pir
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad3.pir
funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad5.pir
funvip/external/MAFFT_Windows/mafft-win/mafft-signed.ps1
funvip/external/MAFFT_Windows/mafft-win/mafft.bat
funvip/external/MAFFT_Windows/mafft-win/testdata.txt
funvip/external/MAFFT_Windows/mafft-win/usr/bin/awk.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/basename.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/bash.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/cat.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/chmod.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/comm.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/cp.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/cut.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/date.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/dirname.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/echo.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/env.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/expr.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/false.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/file.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/fold.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/grep.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/gzip.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/head.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/id.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/info.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/join.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/ln.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/ls.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/mafft
funvip/external/MAFFT_Windows/mafft-win/usr/bin/mafft-homologs.rb
funvip/external/MAFFT_Windows/mafft-win/usr/bin/md5sum.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/mkdir.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/mktemp.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/more.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-2.0.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-gcc_s-seh-1.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-gmp-10.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-iconv-2.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-intl-8.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-magic-1.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-mpfr-4.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-ncursesw6.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-pcre-1.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-readline6.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/msys-z.dll
funvip/external/MAFFT_Windows/mafft-win/usr/bin/mv.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/od.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/paste.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/printf.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/ps.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/pwd.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/rm.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/rmdir.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/sed.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/sh.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/sleep.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/sort.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/split.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/stty.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/tail.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/tar.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/touch.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/tr.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/true.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/uname.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/uniq.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/wc.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/which.exe
funvip/external/MAFFT_Windows/mafft-win/usr/bin/xargs.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/addsingle.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/contrafoldwrap.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/countlen.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/dash_client.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/disttbfast.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/dndblast.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/dndfast7.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/dndpre.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/dvtditr.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/f2cl.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/filter.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/getlag.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/hex2maffttext.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/mafft-distance.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/mafft-homologs.1
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/mafft-profile.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/mafft.1
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/mafftash_premafft.pl
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/maffttext2hex.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/makedirectionlist.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/mccaskillwrap.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/multi2hat3s.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/nodepair.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/pairash.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/pairlocalalign.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/regtable2seq.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/replaceu.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/restoreu.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/score.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/seekquencer_premafft.pl
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/seq2regtable.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/setcore.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/setdirection.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/sextet5.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/splittbfast.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/tbfast.exe
funvip/external/MAFFT_Windows/mafft-win/usr/lib/mafft/version.exe
funvip/external/MAFFT_Windows/mafft-win/usr/share/misc/magic
funvip/external/RAxML_Windows/GPL-3.0.txt
funvip/external/RAxML_Windows/README
funvip/external/RAxML_Windows/raxmlHPC-PTHREADS-AVX2.exe
funvip/external/iqtree/example.cf
funvip/external/iqtree/example.nex
funvip/external/iqtree/example.phy
funvip/external/iqtree/models.nex
funvip/external/iqtree/bin/iqtree2-click.exe
funvip/external/iqtree/bin/iqtree2.exe
funvip/external/iqtree/bin/libiomp5md.dll
funvip/external/mmseqs_Windows/LICENSE.md
funvip/external/mmseqs_Windows/README.md
funvip/external/mmseqs_Windows/mmseqs.bat
funvip/external/mmseqs_Windows/bin/busybox.exe
funvip/external/mmseqs_Windows/bin/cygbz2-1.dll
funvip/external/mmseqs_Windows/bin/cyggcc_s-seh-1.dll
funvip/external/mmseqs_Windows/bin/cyggomp-1.dll
funvip/external/mmseqs_Windows/bin/cygstdc++-6.dll
funvip/external/mmseqs_Windows/bin/cygwin1.dll
funvip/external/mmseqs_Windows/bin/cygz.dll
funvip/external/mmseqs_Windows/bin/mmseqs.exe
funvip/external/mmseqs_Windows/examples/QUERY.fasta
funvip/external/mmseqs_Windows/matrices/PAM10.out
funvip/external/mmseqs_Windows/matrices/PAM100.out
funvip/external/mmseqs_Windows/matrices/PAM110.out
funvip/external/mmseqs_Windows/matrices/PAM120.out
funvip/external/mmseqs_Windows/matrices/PAM130.out
funvip/external/mmseqs_Windows/matrices/PAM140.out
funvip/external/mmseqs_Windows/matrices/PAM150.out
funvip/external/mmseqs_Windows/matrices/PAM160.out
funvip/external/mmseqs_Windows/matrices/PAM170.out
funvip/external/mmseqs_Windows/matrices/PAM180.out
funvip/external/mmseqs_Windows/matrices/PAM190.out
funvip/external/mmseqs_Windows/matrices/PAM20.out
funvip/external/mmseqs_Windows/matrices/PAM30.out
funvip/external/mmseqs_Windows/matrices/PAM40.out
funvip/external/mmseqs_Windows/matrices/PAM50.out
funvip/external/mmseqs_Windows/matrices/PAM60.out
funvip/external/mmseqs_Windows/matrices/PAM70.out
funvip/external/mmseqs_Windows/matrices/PAM80.out
funvip/external/mmseqs_Windows/matrices/PAM90.out
funvip/external/mmseqs_Windows/matrices/VTML10.out
funvip/external/mmseqs_Windows/matrices/VTML120.out
funvip/external/mmseqs_Windows/matrices/VTML160.out
funvip/external/mmseqs_Windows/matrices/VTML20.out
funvip/external/mmseqs_Windows/matrices/VTML40.out
funvip/external/mmseqs_Windows/matrices/VTML80.out
funvip/external/mmseqs_Windows/matrices/blosum100.out
funvip/external/mmseqs_Windows/matrices/blosum30.out
funvip/external/mmseqs_Windows/matrices/blosum35.out
funvip/external/mmseqs_Windows/matrices/blosum40.out
funvip/external/mmseqs_Windows/matrices/blosum45.out
funvip/external/mmseqs_Windows/matrices/blosum50.out
funvip/external/mmseqs_Windows/matrices/blosum55.out
funvip/external/mmseqs_Windows/matrices/blosum60.out
funvip/external/mmseqs_Windows/matrices/blosum62.out
funvip/external/mmseqs_Windows/matrices/blosum65.out
funvip/external/mmseqs_Windows/matrices/blosum70.out
funvip/external/mmseqs_Windows/matrices/blosum75.out
funvip/external/mmseqs_Windows/matrices/blosum80.out
funvip/external/mmseqs_Windows/matrices/blosum85.out
funvip/external/mmseqs_Windows/matrices/blosum90.out
funvip/external/mmseqs_Windows/matrices/blosum95.out
funvip/external/mmseqs_Windows/matrices/nucleotide.out
funvip/external/mmseqs_Windows/util/bash-completion.sh
funvip/external/modeltest-ng_Windows/cyggcc_s-seh-1.dll
funvip/external/modeltest-ng_Windows/cygstdc++-6.dll
funvip/external/modeltest-ng_Windows/cygwin1.dll
funvip/external/modeltest-ng_Windows/modeltest-ng.exe
funvip/external/trimal.v1.4/trimAl/AUTHORS
funvip/external/trimal.v1.4/trimAl/CHANGELOG
funvip/external/trimal.v1.4/trimAl/LICENSE
funvip/external/trimal.v1.4/trimAl/README
funvip/external/trimal.v1.4/trimAl/bin/libgcc_s_dw2-1.dll
funvip/external/trimal.v1.4/trimAl/bin/libstdc++-6.dll
funvip/external/trimal.v1.4/trimAl/bin/trimal.exe
funvip/external/trimal.v1.4/trimAl/scripts/check_codon_alignments.py
funvip/external/trimal.v1.4/trimAl/scripts/compare_trimmed_msas.sh
funvip/external/trimal.v1.4/trimAl/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py
funvip/external/trimal.v1.4/trimAl/scripts/generate_trimmed_msas.sh
funvip/external/trimal.v1.4/trimAl/scripts/get_sequence_representative_from_alignment.py
funvip/external/trimal.v1.4/trimAl/scripts/get_sequences_gaps_ratio.py
funvip/external/trimal.v1.4/trimAl/scripts/remove_shorter_sequences.py
funvip/external/trimal.v1.4/trimAl/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py
funvip/external/trimal.v1.4/trimAl/scripts/set_manual_boundaries.py
funvip/external/trimal.v1.4/trimAl/source/alignment.cpp
funvip/external/trimal.v1.4/trimAl/source/alignment.h
funvip/external/trimal.v1.4/trimAl/source/alignment.o
funvip/external/trimal.v1.4/trimAl/source/autAlignment.cpp
funvip/external/trimal.v1.4/trimAl/source/autAlignment.o
funvip/external/trimal.v1.4/trimAl/source/compareFiles.cpp
funvip/external/trimal.v1.4/trimAl/source/compareFiles.h
funvip/external/trimal.v1.4/trimAl/source/compareFiles.o
funvip/external/trimal.v1.4/trimAl/source/defines.h
funvip/external/trimal.v1.4/trimAl/source/main.cpp
funvip/external/trimal.v1.4/trimAl/source/makefile
funvip/external/trimal.v1.4/trimAl/source/makefile.MacOS
funvip/external/trimal.v1.4/trimAl/source/readAl.cpp
funvip/external/trimal.v1.4/trimAl/source/readal.exe
funvip/external/trimal.v1.4/trimAl/source/rwAlignment.cpp
funvip/external/trimal.v1.4/trimAl/source/rwAlignment.o
funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.cpp
funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.h
funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.o
funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.cpp
funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.h
funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.o
funvip/external/trimal.v1.4/trimAl/source/statAl.cpp
funvip/external/trimal.v1.4/trimAl/source/statal.exe
funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.cpp
funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.h
funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.o
funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.cpp
funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.h
funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.cpp
funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.h
funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.o
funvip/external/trimal.v1.4/trimAl/source/utils.cpp
funvip/external/trimal.v1.4/trimAl/source/utils.h
funvip/external/trimal.v1.4/trimAl/source/utils.o
funvip/external/trimal.v1.4/trimAl/source/values.h
funvip/preset/.gitignore
funvip/preset/accurate.yaml
funvip/preset/fast.yaml
funvip/src/.gitignore
funvip/src/__init__.py
funvip/src/align.py
funvip/src/cluster.py
funvip/src/command.py
funvip/src/concatenate.py
funvip/src/dataset.py
funvip/src/exceptions.py
funvip/src/ext.py
funvip/src/hasher.py
funvip/src/initialize.py
funvip/src/logger.py
funvip/src/logics.py
funvip/src/modeltest.py
funvip/src/opt_generator.py
funvip/src/reporter.py
funvip/src/save.py
funvip/src/search.py
funvip/src/tool.py
funvip/src/tree.py
funvip/src/tree_interpretation.py
funvip/src/tree_interpretation_pipe.py
funvip/src/trim.py
funvip/src/validate_input.py
funvip/src/validate_option.py
funvip/src/version.py
funvip/src/templates/template.html
funvip/test_dataset/penicillium/Options.config
funvip/test_dataset/penicillium/preset.yaml
funvip/test_dataset/penicillium/DB/DB_Penicillium.xlsx
funvip/test_dataset/penicillium/Query/Query.xlsx
funvip/test_dataset/sanghuangporus/preset.yaml
funvip/test_dataset/sanghuangporus/DB/FunVIP_Sanghuangporus_db.xlsx
funvip/test_dataset/sanghuangporus/Query/FunVIP_Sanghuangporus_query.xlsx
funvip/test_dataset/terrei/preset.yaml
funvip/test_dataset/terrei/DB/FunVIP_Aspergillus_db.xlsx
funvip/test_dataset/terrei/Query/FunVIP_Aspergillus_query.xlsx
tests/test_cluster.py
tests/test_dataset.py
tests/test_hasher.py
tests/test_integration_terrei.py
tests/test_logics.py
tests/test_reporter.py
tests/test_tool.py
tests/test_validate_option.py