FunVIP 0.3.20__tar.gz → 0.3.21__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (193) hide show
  1. {funvip-0.3.20 → funvip-0.3.21/FunVIP.egg-info}/PKG-INFO +1 -1
  2. funvip-0.3.21/FunVIP.egg-info/SOURCES.txt +189 -0
  3. funvip-0.3.21/FunVIP.egg-info/top_level.txt +1 -0
  4. {funvip-0.3.20/funvip/FunVIP.egg-info → funvip-0.3.21}/PKG-INFO +1 -1
  5. funvip-0.3.21/funvip/FunVIP_GUI.py +525 -0
  6. funvip-0.3.21/funvip/data/Option_manager.xlsx +0 -0
  7. funvip-0.3.21/funvip/data/genus_line.txt +3095 -0
  8. funvip-0.3.21/funvip/external/BLAST_Windows/Uninstall-ncbi-blast-2.12.0+.exe +0 -0
  9. funvip-0.3.21/funvip/external/BLAST_Windows/bin/blastn.exe +0 -0
  10. funvip-0.3.21/funvip/external/BLAST_Windows/bin/get_species_taxids.sh +152 -0
  11. funvip-0.3.21/funvip/external/BLAST_Windows/bin/legacy_blast.pl +1359 -0
  12. funvip-0.3.21/funvip/external/BLAST_Windows/bin/makeblastdb.exe +0 -0
  13. funvip-0.3.21/funvip/external/BLAST_Windows/bin/nghttp2.dll +0 -0
  14. funvip-0.3.21/funvip/external/BLAST_Windows/bin/update_blastdb.pl +1069 -0
  15. funvip-0.3.21/funvip/external/BLAST_Windows/doc/README.txt +2 -0
  16. funvip-0.3.21/funvip/external/FastTree_Windows/FastTree.exe +0 -0
  17. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Documentation/Gblocks_documentation.html +598 -0
  18. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Gblocks.exe +0 -0
  19. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cox2.pir +170 -0
  20. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cytb.pir +187 -0
  21. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad3.pir +102 -0
  22. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad5.pir +289 -0
  23. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/nad3.pir +101 -0
  24. funvip-0.3.21/funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/paths +4 -0
  25. funvip-0.3.21/funvip/external/MAFFT_LICENSE +674 -0
  26. funvip-0.3.21/funvip/external/MAFFT_Windows.zip +0 -0
  27. funvip-0.3.21/funvip/external/RAxML_Windows/GPL-3.0.txt +674 -0
  28. funvip-0.3.21/funvip/external/RAxML_Windows/README +3 -0
  29. funvip-0.3.21/funvip/external/RAxML_Windows/raxmlHPC-PTHREADS-AVX2.exe +0 -0
  30. funvip-0.3.21/funvip/external/iqtree/bin/iqtree2-click.exe +0 -0
  31. funvip-0.3.21/funvip/external/iqtree/bin/iqtree2.exe +0 -0
  32. funvip-0.3.21/funvip/external/iqtree/bin/libiomp5md.dll +0 -0
  33. funvip-0.3.21/funvip/external/iqtree/example.cf +18852 -0
  34. funvip-0.3.21/funvip/external/iqtree/example.nex +9 -0
  35. funvip-0.3.21/funvip/external/iqtree/example.phy +18 -0
  36. funvip-0.3.21/funvip/external/iqtree/models.nex +955 -0
  37. funvip-0.3.21/funvip/external/mmseqs_Windows/LICENSE.md +674 -0
  38. funvip-0.3.21/funvip/external/mmseqs_Windows/README.md +141 -0
  39. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/busybox.exe +0 -0
  40. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/cygbz2-1.dll +0 -0
  41. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/cyggcc_s-seh-1.dll +0 -0
  42. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/cyggomp-1.dll +0 -0
  43. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/cygstdc++-6.dll +0 -0
  44. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/cygwin1.dll +0 -0
  45. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/cygz.dll +0 -0
  46. funvip-0.3.21/funvip/external/mmseqs_Windows/bin/mmseqs.exe +0 -0
  47. funvip-0.3.21/funvip/external/mmseqs_Windows/examples/QUERY.fasta +1000 -0
  48. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM10.out +23 -0
  49. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM100.out +23 -0
  50. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM110.out +23 -0
  51. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM120.out +23 -0
  52. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM130.out +23 -0
  53. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM140.out +23 -0
  54. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM150.out +23 -0
  55. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM160.out +23 -0
  56. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM170.out +23 -0
  57. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM180.out +23 -0
  58. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM190.out +23 -0
  59. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM20.out +23 -0
  60. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM30.out +25 -0
  61. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM40.out +23 -0
  62. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM50.out +23 -0
  63. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM60.out +23 -0
  64. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM70.out +23 -0
  65. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM80.out +23 -0
  66. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/PAM90.out +23 -0
  67. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/VTML10.out +34 -0
  68. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/VTML120.out +34 -0
  69. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/VTML160.out +34 -0
  70. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/VTML20.out +33 -0
  71. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/VTML40.out +34 -0
  72. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/VTML80.out +35 -0
  73. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum100.out +23 -0
  74. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum30.out +23 -0
  75. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum35.out +23 -0
  76. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum40.out +23 -0
  77. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum45.out +23 -0
  78. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum50.out +23 -0
  79. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum55.out +23 -0
  80. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum60.out +23 -0
  81. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum62.out +25 -0
  82. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum65.out +23 -0
  83. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum70.out +23 -0
  84. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum75.out +23 -0
  85. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum80.out +23 -0
  86. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum85.out +23 -0
  87. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum90.out +23 -0
  88. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/blosum95.out +23 -0
  89. funvip-0.3.21/funvip/external/mmseqs_Windows/matrices/nucleotide.out +9 -0
  90. funvip-0.3.21/funvip/external/mmseqs_Windows/mmseqs.bat +28 -0
  91. funvip-0.3.21/funvip/external/mmseqs_Windows/util/bash-completion.sh +18 -0
  92. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/AUTHORS +16 -0
  93. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/CHANGELOG +150 -0
  94. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/LICENSE +674 -0
  95. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/README +16 -0
  96. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/bin/libgcc_s_dw2-1.dll +0 -0
  97. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/bin/libstdc++-6.dll +0 -0
  98. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/bin/trimal.exe +0 -0
  99. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/check_codon_alignments.py +107 -0
  100. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/compare_trimmed_msas.sh +10 -0
  101. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py +143 -0
  102. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/generate_trimmed_msas.sh +512 -0
  103. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/get_sequence_representative_from_alignment.py +95 -0
  104. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/get_sequences_gaps_ratio.py +78 -0
  105. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/remove_shorter_sequences.py +73 -0
  106. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py +273 -0
  107. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/scripts/set_manual_boundaries.py +198 -0
  108. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/alignment.cpp +3378 -0
  109. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/alignment.h +546 -0
  110. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/alignment.o +0 -0
  111. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/autAlignment.cpp +448 -0
  112. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/autAlignment.o +0 -0
  113. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/compareFiles.cpp +518 -0
  114. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/compareFiles.h +51 -0
  115. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/compareFiles.o +0 -0
  116. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/defines.h +54 -0
  117. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/main.cpp +1973 -0
  118. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/makefile +50 -0
  119. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/makefile.MacOS +53 -0
  120. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/readAl.cpp +383 -0
  121. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/readal.exe +0 -0
  122. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/rwAlignment.cpp +2253 -0
  123. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/rwAlignment.o +0 -0
  124. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.cpp +209 -0
  125. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.h +117 -0
  126. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.o +0 -0
  127. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.cpp +463 -0
  128. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.h +70 -0
  129. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.o +0 -0
  130. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statAl.cpp +574 -0
  131. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statal.exe +0 -0
  132. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.cpp +428 -0
  133. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.h +112 -0
  134. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.o +0 -0
  135. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.cpp +56 -0
  136. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.h +48 -0
  137. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.cpp +464 -0
  138. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.h +87 -0
  139. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.o +0 -0
  140. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/utils.cpp +850 -0
  141. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/utils.h +207 -0
  142. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/utils.o +0 -0
  143. funvip-0.3.21/funvip/external/trimal.v1.4/trimAl/source/values.h +119 -0
  144. funvip-0.3.21/funvip/main.py +402 -0
  145. funvip-0.3.21/funvip/preset/accurate.yaml +30 -0
  146. funvip-0.3.21/funvip/preset/fast.yaml +25 -0
  147. funvip-0.3.21/funvip/src/__init__.py +0 -0
  148. funvip-0.3.21/funvip/test_dataset/penicillium/DB/DB_Penicillium.xlsx +0 -0
  149. funvip-0.3.21/funvip/test_dataset/penicillium/Options.config +83 -0
  150. funvip-0.3.21/funvip/test_dataset/penicillium/Query/Query.xlsx +0 -0
  151. funvip-0.3.21/funvip/test_dataset/penicillium/preset.yaml +40 -0
  152. funvip-0.3.21/funvip/test_dataset/terrei/DB/FunVIP_Aspergillus_db.xlsx +0 -0
  153. funvip-0.3.21/funvip/test_dataset/terrei/Query/FunVIP_Aspergillus_query.xlsx +0 -0
  154. funvip-0.3.21/funvip/test_dataset/terrei/preset.yaml +39 -0
  155. {funvip-0.3.20 → funvip-0.3.21}/pyproject.toml +9 -8
  156. funvip-0.3.20/funvip/FunVIP.egg-info/SOURCES.txt +0 -39
  157. funvip-0.3.20/funvip/FunVIP.egg-info/top_level.txt +0 -5
  158. {funvip-0.3.20/funvip → funvip-0.3.21}/FunVIP.egg-info/dependency_links.txt +0 -0
  159. {funvip-0.3.20/funvip → funvip-0.3.21}/FunVIP.egg-info/entry_points.txt +0 -0
  160. {funvip-0.3.20/funvip → funvip-0.3.21}/FunVIP.egg-info/requires.txt +0 -0
  161. {funvip-0.3.20 → funvip-0.3.21}/LICENSE +0 -0
  162. {funvip-0.3.20 → funvip-0.3.21}/README.md +0 -0
  163. {funvip-0.3.20/funvip/data → funvip-0.3.21/funvip}/__init__.py +0 -0
  164. {funvip-0.3.20/funvip/external → funvip-0.3.21/funvip/data}/__init__.py +0 -0
  165. {funvip-0.3.20 → funvip-0.3.21}/funvip/external/BLAST_Windows/bin/cleanup-blastdb-volumes.py +0 -0
  166. {funvip-0.3.20/funvip/src → funvip-0.3.21/funvip/external}/__init__.py +0 -0
  167. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/align.py +0 -0
  168. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/cluster.py +0 -0
  169. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/command.py +0 -0
  170. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/concatenate.py +0 -0
  171. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/dataset.py +0 -0
  172. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/ext.py +0 -0
  173. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/hasher.py +0 -0
  174. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/initialize.py +0 -0
  175. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/logger.py +0 -0
  176. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/logics.py +0 -0
  177. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/modeltest.py +0 -0
  178. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/ncbi.py +0 -0
  179. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/opt_generator.py +0 -0
  180. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/patch.py +0 -0
  181. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/reporter.py +0 -0
  182. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/save.py +0 -0
  183. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/search.py +0 -0
  184. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/tool.py +0 -0
  185. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/tree.py +0 -0
  186. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/tree_interpretation.py +0 -0
  187. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/tree_interpretation_pipe.py +0 -0
  188. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/trim.py +0 -0
  189. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/validate_input.py +0 -0
  190. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/validate_option.py +0 -0
  191. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/validation.py +0 -0
  192. {funvip-0.3.20 → funvip-0.3.21}/funvip/src/version.py +0 -0
  193. {funvip-0.3.20 → funvip-0.3.21}/setup.cfg +0 -0
{funvip-0.3.20 → funvip-0.3.21/FunVIP.egg-info}/PKG-INFO RENAMED
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  Metadata-Version: 2.1
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  Name: FunVIP
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- Version: 0.3.20
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+ Version: 0.3.21
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  Summary: Fungal Validation & Identification Pipeline
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  Author-email: Changwan Seo <wan101010@snu.ac.kr>
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  License: GPL-3.0
funvip-0.3.21/FunVIP.egg-info/SOURCES.txt ADDED
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+ LICENSE
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+ README.md
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+ pyproject.toml
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+ FunVIP.egg-info/PKG-INFO
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+ FunVIP.egg-info/SOURCES.txt
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+ FunVIP.egg-info/dependency_links.txt
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+ FunVIP.egg-info/entry_points.txt
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+ FunVIP.egg-info/requires.txt
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+ FunVIP.egg-info/top_level.txt
10
+ funvip/FunVIP_GUI.py
11
+ funvip/__init__.py
12
+ funvip/main.py
13
+ funvip/data/Option_manager.xlsx
14
+ funvip/data/__init__.py
15
+ funvip/data/genus_line.txt
16
+ funvip/external/MAFFT_LICENSE
17
+ funvip/external/MAFFT_Windows.zip
18
+ funvip/external/__init__.py
19
+ funvip/external/BLAST_Windows/Uninstall-ncbi-blast-2.12.0+.exe
20
+ funvip/external/BLAST_Windows/bin/blastn.exe
21
+ funvip/external/BLAST_Windows/bin/cleanup-blastdb-volumes.py
22
+ funvip/external/BLAST_Windows/bin/get_species_taxids.sh
23
+ funvip/external/BLAST_Windows/bin/legacy_blast.pl
24
+ funvip/external/BLAST_Windows/bin/makeblastdb.exe
25
+ funvip/external/BLAST_Windows/bin/nghttp2.dll
26
+ funvip/external/BLAST_Windows/bin/update_blastdb.pl
27
+ funvip/external/BLAST_Windows/doc/README.txt
28
+ funvip/external/FastTree_Windows/FastTree.exe
29
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Gblocks.exe
30
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/nad3.pir
31
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/paths
32
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/Documentation/Gblocks_documentation.html
33
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cox2.pir
34
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/cytb.pir
35
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad3.pir
36
+ funvip/external/Gblocks_Windows_0.91b/Gblocks_0.91b/more_alignments/nad5.pir
37
+ funvip/external/RAxML_Windows/GPL-3.0.txt
38
+ funvip/external/RAxML_Windows/README
39
+ funvip/external/RAxML_Windows/raxmlHPC-PTHREADS-AVX2.exe
40
+ funvip/external/iqtree/example.cf
41
+ funvip/external/iqtree/example.nex
42
+ funvip/external/iqtree/example.phy
43
+ funvip/external/iqtree/models.nex
44
+ funvip/external/iqtree/bin/iqtree2-click.exe
45
+ funvip/external/iqtree/bin/iqtree2.exe
46
+ funvip/external/iqtree/bin/libiomp5md.dll
47
+ funvip/external/mmseqs_Windows/LICENSE.md
48
+ funvip/external/mmseqs_Windows/README.md
49
+ funvip/external/mmseqs_Windows/mmseqs.bat
50
+ funvip/external/mmseqs_Windows/bin/busybox.exe
51
+ funvip/external/mmseqs_Windows/bin/cygbz2-1.dll
52
+ funvip/external/mmseqs_Windows/bin/cyggcc_s-seh-1.dll
53
+ funvip/external/mmseqs_Windows/bin/cyggomp-1.dll
54
+ funvip/external/mmseqs_Windows/bin/cygstdc++-6.dll
55
+ funvip/external/mmseqs_Windows/bin/cygwin1.dll
56
+ funvip/external/mmseqs_Windows/bin/cygz.dll
57
+ funvip/external/mmseqs_Windows/bin/mmseqs.exe
58
+ funvip/external/mmseqs_Windows/examples/QUERY.fasta
59
+ funvip/external/mmseqs_Windows/matrices/PAM10.out
60
+ funvip/external/mmseqs_Windows/matrices/PAM100.out
61
+ funvip/external/mmseqs_Windows/matrices/PAM110.out
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+ funvip/external/mmseqs_Windows/matrices/PAM120.out
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+ funvip/external/mmseqs_Windows/matrices/PAM130.out
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+ funvip/external/mmseqs_Windows/matrices/PAM140.out
65
+ funvip/external/mmseqs_Windows/matrices/PAM150.out
66
+ funvip/external/mmseqs_Windows/matrices/PAM160.out
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+ funvip/external/mmseqs_Windows/matrices/PAM170.out
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+ funvip/external/mmseqs_Windows/matrices/PAM180.out
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+ funvip/external/mmseqs_Windows/matrices/PAM190.out
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+ funvip/external/mmseqs_Windows/matrices/PAM20.out
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+ funvip/external/mmseqs_Windows/matrices/PAM30.out
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+ funvip/external/mmseqs_Windows/matrices/PAM40.out
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+ funvip/external/mmseqs_Windows/matrices/PAM50.out
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+ funvip/external/mmseqs_Windows/matrices/PAM60.out
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+ funvip/external/mmseqs_Windows/matrices/PAM70.out
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+ funvip/external/mmseqs_Windows/matrices/PAM80.out
77
+ funvip/external/mmseqs_Windows/matrices/PAM90.out
78
+ funvip/external/mmseqs_Windows/matrices/VTML10.out
79
+ funvip/external/mmseqs_Windows/matrices/VTML120.out
80
+ funvip/external/mmseqs_Windows/matrices/VTML160.out
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+ funvip/external/mmseqs_Windows/matrices/VTML20.out
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+ funvip/external/mmseqs_Windows/matrices/VTML40.out
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+ funvip/external/mmseqs_Windows/matrices/VTML80.out
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+ funvip/external/mmseqs_Windows/matrices/blosum100.out
85
+ funvip/external/mmseqs_Windows/matrices/blosum30.out
86
+ funvip/external/mmseqs_Windows/matrices/blosum35.out
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+ funvip/external/mmseqs_Windows/matrices/blosum40.out
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+ funvip/external/mmseqs_Windows/matrices/blosum45.out
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+ funvip/external/mmseqs_Windows/matrices/blosum50.out
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+ funvip/external/mmseqs_Windows/matrices/blosum55.out
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+ funvip/external/mmseqs_Windows/matrices/blosum60.out
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+ funvip/external/mmseqs_Windows/matrices/blosum62.out
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+ funvip/external/mmseqs_Windows/matrices/blosum65.out
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+ funvip/external/mmseqs_Windows/matrices/blosum70.out
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+ funvip/external/mmseqs_Windows/matrices/blosum75.out
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+ funvip/external/mmseqs_Windows/matrices/blosum80.out
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+ funvip/external/mmseqs_Windows/matrices/blosum85.out
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+ funvip/external/mmseqs_Windows/matrices/blosum90.out
99
+ funvip/external/mmseqs_Windows/matrices/blosum95.out
100
+ funvip/external/mmseqs_Windows/matrices/nucleotide.out
101
+ funvip/external/mmseqs_Windows/util/bash-completion.sh
102
+ funvip/external/trimal.v1.4/trimAl/AUTHORS
103
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104
+ funvip/external/trimal.v1.4/trimAl/LICENSE
105
+ funvip/external/trimal.v1.4/trimAl/README
106
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107
+ funvip/external/trimal.v1.4/trimAl/bin/libstdc++-6.dll
108
+ funvip/external/trimal.v1.4/trimAl/bin/trimal.exe
109
+ funvip/external/trimal.v1.4/trimAl/scripts/check_codon_alignments.py
110
+ funvip/external/trimal.v1.4/trimAl/scripts/compare_trimmed_msas.sh
111
+ funvip/external/trimal.v1.4/trimAl/scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py
112
+ funvip/external/trimal.v1.4/trimAl/scripts/generate_trimmed_msas.sh
113
+ funvip/external/trimal.v1.4/trimAl/scripts/get_sequence_representative_from_alignment.py
114
+ funvip/external/trimal.v1.4/trimAl/scripts/get_sequences_gaps_ratio.py
115
+ funvip/external/trimal.v1.4/trimAl/scripts/remove_shorter_sequences.py
116
+ funvip/external/trimal.v1.4/trimAl/scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py
117
+ funvip/external/trimal.v1.4/trimAl/scripts/set_manual_boundaries.py
118
+ funvip/external/trimal.v1.4/trimAl/source/alignment.cpp
119
+ funvip/external/trimal.v1.4/trimAl/source/alignment.h
120
+ funvip/external/trimal.v1.4/trimAl/source/alignment.o
121
+ funvip/external/trimal.v1.4/trimAl/source/autAlignment.cpp
122
+ funvip/external/trimal.v1.4/trimAl/source/autAlignment.o
123
+ funvip/external/trimal.v1.4/trimAl/source/compareFiles.cpp
124
+ funvip/external/trimal.v1.4/trimAl/source/compareFiles.h
125
+ funvip/external/trimal.v1.4/trimAl/source/compareFiles.o
126
+ funvip/external/trimal.v1.4/trimAl/source/defines.h
127
+ funvip/external/trimal.v1.4/trimAl/source/main.cpp
128
+ funvip/external/trimal.v1.4/trimAl/source/makefile
129
+ funvip/external/trimal.v1.4/trimAl/source/makefile.MacOS
130
+ funvip/external/trimal.v1.4/trimAl/source/readAl.cpp
131
+ funvip/external/trimal.v1.4/trimAl/source/readal.exe
132
+ funvip/external/trimal.v1.4/trimAl/source/rwAlignment.cpp
133
+ funvip/external/trimal.v1.4/trimAl/source/rwAlignment.o
134
+ funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.cpp
135
+ funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.h
136
+ funvip/external/trimal.v1.4/trimAl/source/sequencesMatrix.o
137
+ funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.cpp
138
+ funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.h
139
+ funvip/external/trimal.v1.4/trimAl/source/similarityMatrix.o
140
+ funvip/external/trimal.v1.4/trimAl/source/statAl.cpp
141
+ funvip/external/trimal.v1.4/trimAl/source/statal.exe
142
+ funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.cpp
143
+ funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.h
144
+ funvip/external/trimal.v1.4/trimAl/source/statisticsConservation.o
145
+ funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.cpp
146
+ funvip/external/trimal.v1.4/trimAl/source/statisticsFiles.h
147
+ funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.cpp
148
+ funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.h
149
+ funvip/external/trimal.v1.4/trimAl/source/statisticsGaps.o
150
+ funvip/external/trimal.v1.4/trimAl/source/utils.cpp
151
+ funvip/external/trimal.v1.4/trimAl/source/utils.h
152
+ funvip/external/trimal.v1.4/trimAl/source/utils.o
153
+ funvip/external/trimal.v1.4/trimAl/source/values.h
154
+ funvip/preset/accurate.yaml
155
+ funvip/preset/fast.yaml
156
+ funvip/src/__init__.py
157
+ funvip/src/align.py
158
+ funvip/src/cluster.py
159
+ funvip/src/command.py
160
+ funvip/src/concatenate.py
161
+ funvip/src/dataset.py
162
+ funvip/src/ext.py
163
+ funvip/src/hasher.py
164
+ funvip/src/initialize.py
165
+ funvip/src/logger.py
166
+ funvip/src/logics.py
167
+ funvip/src/modeltest.py
168
+ funvip/src/ncbi.py
169
+ funvip/src/opt_generator.py
170
+ funvip/src/patch.py
171
+ funvip/src/reporter.py
172
+ funvip/src/save.py
173
+ funvip/src/search.py
174
+ funvip/src/tool.py
175
+ funvip/src/tree.py
176
+ funvip/src/tree_interpretation.py
177
+ funvip/src/tree_interpretation_pipe.py
178
+ funvip/src/trim.py
179
+ funvip/src/validate_input.py
180
+ funvip/src/validate_option.py
181
+ funvip/src/validation.py
182
+ funvip/src/version.py
183
+ funvip/test_dataset/penicillium/Options.config
184
+ funvip/test_dataset/penicillium/preset.yaml
185
+ funvip/test_dataset/penicillium/DB/DB_Penicillium.xlsx
186
+ funvip/test_dataset/penicillium/Query/Query.xlsx
187
+ funvip/test_dataset/terrei/preset.yaml
188
+ funvip/test_dataset/terrei/DB/FunVIP_Aspergillus_db.xlsx
189
+ funvip/test_dataset/terrei/Query/FunVIP_Aspergillus_query.xlsx
funvip-0.3.21/FunVIP.egg-info/top_level.txt ADDED
@@ -0,0 +1 @@
1
+ funvip
{funvip-0.3.20/funvip/FunVIP.egg-info → funvip-0.3.21}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: FunVIP
3
- Version: 0.3.20
3
+ Version: 0.3.21
4
4
  Summary: Fungal Validation & Identification Pipeline
5
5
  Author-email: Changwan Seo <wan101010@snu.ac.kr>
6
6
  License: GPL-3.0