data/paleomix-1.3.2/CHANGES.md:275: nessesary ==> necessary data/paleomix-1.3.2/CHANGES.md:505: seperately ==> separately data/paleomix-1.3.2/CHANGES.md:526: aviod ==> avoid data/paleomix-1.3.2/CHANGES.md:530: preperation ==> preparation data/paleomix-1.3.2/CHANGES.md:531: seperate ==> separate data/paleomix-1.3.2/CHANGES.md:620: serveral ==> several data/paleomix-1.3.2/CHANGES.md:700: recieve ==> receive data/paleomix-1.3.2/docs/examples.rst:70: nessesary ==> necessary data/paleomix-1.3.2/docs/introduction.rst:19: faciliate ==> facilitate data/paleomix-1.3.2/docs/bam_pipeline/makefile.rst:140: nessesarily ==> necessarily data/paleomix-1.3.2/docs/bam_pipeline/makefile.rst:251: wether ==> weather, whether data/paleomix-1.3.2/docs/bam_pipeline/requirements.rst:19: Jave ==> Java, have data/paleomix-1.3.2/docs/bam_pipeline/usage.rst:93: eiter ==> either data/paleomix-1.3.2/docs/bam_pipeline/usage.rst:223: Fiels ==> Feels, fields, files, phials data/paleomix-1.3.2/docs/phylo_pipeline/overview.rst:21: partioned ==> partitioned data/paleomix-1.3.2/docs/phylo_pipeline/usage.rst:101: nessesary ==> necessary data/paleomix-1.3.2/docs/phylo_pipeline/usage.rst:101: nessesary ==> necessary data/paleomix-1.3.2/docs/phylo_pipeline/usage.rst:131: likelyhood ==> likelihood data/paleomix-1.3.2/docs/phylo_pipeline/usage.rst:201: excuted ==> executed data/paleomix-1.3.2/docs/troubleshooting/common.rst:46: nessesary ==> necessary data/paleomix-1.3.2/docs/troubleshooting/common.rst:73: excuted ==> executed data/paleomix-1.3.2/docs/troubleshooting/common.rst:108: sting ==> string data/paleomix-1.3.2/docs/zonkey_pipeline/panel.rst:43: SOM ==> SOME data/paleomix-1.3.2/docs/zonkey_pipeline/panel.rst:93: requried ==> required data/paleomix-1.3.2/docs/zonkey_pipeline/panel.rst:140: adviced ==> advised data/paleomix-1.3.2/docs/zonkey_pipeline/panel.rst:167: emperical ==> empirical data/paleomix-1.3.2/docs/zonkey_pipeline/usage.rst:25: seperately ==> separately data/paleomix-1.3.2/docs/zonkey_pipeline/usage.rst:25: madatory ==> mandatory data/paleomix-1.3.2/docs/zonkey_pipeline/usage.rst:28: seperated ==> separated data/paleomix-1.3.2/docs/zonkey_pipeline/usage.rst:31: excuting ==> executing data/paleomix-1.3.2/misc/synthesize_reads.py:147: fragmnet ==> fragment data/paleomix-1.3.2/paleomix/nodegraph.py:35: existance ==> existence data/paleomix-1.3.2/paleomix/nodegraph.py:38: consistant ==> consistent data/paleomix-1.3.2/paleomix/nodegraph.py:263: dependant ==> dependent data/paleomix-1.3.2/paleomix/nodegraph.py:387: nessesary ==> necessary data/paleomix-1.3.2/paleomix/pipeline.py:55: recieved ==> received data/paleomix-1.3.2/paleomix/pipeline.py:321: occured ==> occurred data/paleomix-1.3.2/paleomix/atomiccmd/builder.py:47: seperator ==> separator data/paleomix-1.3.2/paleomix/atomiccmd/builder.py:48: seperate ==> separate data/paleomix-1.3.2/paleomix/atomiccmd/builder.py:95: Attemping ==> Attempting data/paleomix-1.3.2/paleomix/atomiccmd/command.py:49: succesful ==> successful data/paleomix-1.3.2/paleomix/atomiccmd/command.py:50: accidential ==> accidental data/paleomix-1.3.2/paleomix/atomiccmd/command.py:88: Auxillery ==> Auxiliary data/paleomix-1.3.2/paleomix/atomiccmd/command.py:206: recieve ==> receive data/paleomix-1.3.2/paleomix/atomiccmd/command.py:216: wether ==> weather, whether data/paleomix-1.3.2/paleomix/atomiccmd/command.py:216: occured ==> occurred data/paleomix-1.3.2/paleomix/atomiccmd/sets.py:161: forground ==> foreground data/paleomix-1.3.2/paleomix/atomiccmd/sets.py:168: succesfully ==> successfully data/paleomix-1.3.2/paleomix/common/argparse.py:35: setions ==> sections data/paleomix-1.3.2/paleomix/common/bedtools.py:204: defination ==> definition data/paleomix-1.3.2/paleomix/common/fileutils.py:123: enviroment ==> environment data/paleomix-1.3.2/paleomix/common/fileutils.py:312: succesfully ==> successfully data/paleomix-1.3.2/paleomix/common/makefile.py:77: convinience ==> convenience data/paleomix-1.3.2/paleomix/common/makefile.py:168: accidentically ==> accidentally data/paleomix-1.3.2/paleomix/common/makefile.py:629: comparsions ==> comparisons data/paleomix-1.3.2/paleomix/common/makefile.py:729: dictioanry ==> dictionary data/paleomix-1.3.2/paleomix/common/procs.py:105: occured ==> occurred data/paleomix-1.3.2/paleomix/common/sequences.py:28: ambigious ==> ambiguous data/paleomix-1.3.2/paleomix/common/sequences.py:39: ambigious ==> ambiguous data/paleomix-1.3.2/paleomix/common/text.py:68: seperated ==> separated data/paleomix-1.3.2/paleomix/common/utilities.py:146: cummulative ==> cumulative data/paleomix-1.3.2/paleomix/common/vcffilter.py:207: ambigious ==> ambiguous data/paleomix-1.3.2/paleomix/common/vcffilter.py:225: prefering ==> preferring data/paleomix-1.3.2/paleomix/common/vcfwrap.py:57: Wheter ==> Whether data/paleomix-1.3.2/paleomix/common/versions.py:229: contructor ==> constructor data/paleomix-1.3.2/paleomix/common/formats/fastq.py:141: AMBIGIOUS ==> AMBIGUOUS data/paleomix-1.3.2/paleomix/common/formats/fastq.py:154: AMBIGIOUS ==> AMBIGUOUS data/paleomix-1.3.2/paleomix/common/formats/fastq.py:154: AMBIGIOUS ==> AMBIGUOUS data/paleomix-1.3.2/paleomix/common/formats/fastq.py:182: AMBIGIOUS ==> AMBIGUOUS data/paleomix-1.3.2/paleomix/common/formats/newick.py:46: unambigious ==> unambiguous data/paleomix-1.3.2/paleomix/common/formats/newick.py:52: contraints ==> constraints data/paleomix-1.3.2/paleomix/common/formats/newick.py:126: arbitarily ==> arbitrarily data/paleomix-1.3.2/paleomix/common/formats/newick.py:168: unambigious ==> unambiguous data/paleomix-1.3.2/paleomix/common/formats/newick.py:279: parantheses ==> parentheses data/paleomix-1.3.2/paleomix/nodes/bwa.py:303: presense ==> presence data/paleomix-1.3.2/paleomix/nodes/picard.py:36: nessesary ==> necessary data/paleomix-1.3.2/paleomix/nodes/raxml.py:85: nessesary ==> necessary data/paleomix-1.3.2/paleomix/nodes/raxml.py:114: Boostrapping ==> Bootstrapping data/paleomix-1.3.2/paleomix/nodes/samtools.py:63: Unxpected ==> Unexpected data/paleomix-1.3.2/paleomix/nodes/validation.py:206: characterstics ==> characteristics data/paleomix-1.3.2/paleomix/pipelines/bam/config.py:166: Jave ==> Java, have data/paleomix-1.3.2/paleomix/pipelines/bam/pipeline.py:80: exlude ==> exclude, exude data/paleomix-1.3.2/paleomix/pipelines/bam/parts/library.py:41: reponsible ==> responsible data/paleomix-1.3.2/paleomix/pipelines/bam/parts/library.py:46: libray ==> library data/paleomix-1.3.2/paleomix/pipelines/bam/parts/library.py:125: calulate ==> calculate data/paleomix-1.3.2/paleomix/pipelines/phylo/makefile.py:121: specifed ==> specified data/paleomix-1.3.2/paleomix/pipelines/phylo/makefile.py:128: specifed ==> specified data/paleomix-1.3.2/paleomix/pipelines/phylo/makefile.py:306: specifed ==> specified data/paleomix-1.3.2/paleomix/pipelines/phylo/makefile.py:419: assosiated ==> associated data/paleomix-1.3.2/paleomix/pipelines/phylo/makefile.py:453: Determinining ==> Determining data/paleomix-1.3.2/paleomix/pipelines/phylo/mkfile.py:86: seperately ==> separately data/paleomix-1.3.2/paleomix/pipelines/phylo/mkfile.py:165: specfied ==> specified data/paleomix-1.3.2/paleomix/pipelines/phylo/mkfile.py:173: partioned ==> partitioned data/paleomix-1.3.2/paleomix/pipelines/phylo/parts/genotype.py:122: Depenencies ==> Dependencies data/paleomix-1.3.2/paleomix/pipelines/phylo/parts/genotype.py:201: assosiated ==> associated data/paleomix-1.3.2/paleomix/pipelines/phylo/parts/genotype.py:227: retrival ==> retrieval, retrial data/paleomix-1.3.2/paleomix/pipelines/zonkey/database.py:114: emperical ==> empirical data/paleomix-1.3.2/paleomix/pipelines/zonkey/database.py:125: referenc ==> reference data/paleomix-1.3.2/paleomix/pipelines/zonkey/database.py:493: missign ==> missing data/paleomix-1.3.2/paleomix/pipelines/zonkey/pipeline.py:163: strat ==> start, strata data/paleomix-1.3.2/paleomix/pipelines/zonkey/pipeline.py:383: accidential ==> accidental data/paleomix-1.3.2/paleomix/pipelines/zonkey/pipeline.py:470: Sucessfully ==> Successfully data/paleomix-1.3.2/paleomix/pipelines/zonkey/parts/nuclear.py:357: strat ==> start, strata data/paleomix-1.3.2/paleomix/pipelines/zonkey/parts/nuclear.py:358: strat ==> start, strata data/paleomix-1.3.2/paleomix/pipelines/zonkey/parts/nuclear.py:366: strat ==> start, strata data/paleomix-1.3.2/paleomix/pipelines/zonkey/parts/nuclear.py:367: strat ==> start, strata data/paleomix-1.3.2/paleomix/pipelines/zonkey/parts/nuclear.py:393: strat ==> start, strata data/paleomix-1.3.2/paleomix/pipelines/zonkey/parts/summary.py:400: perfomed ==> performed data/paleomix-1.3.2/paleomix/resources/__init__.py:81: Sucessfully ==> Successfully data/paleomix-1.3.2/paleomix/resources/examples/bam_pipeline/makefile.yaml:150: Libray ==> Library data/paleomix-1.3.2/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py:147: fragmnet ==> fragment data/paleomix-1.3.2/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml:62: seperately ==> separately data/paleomix-1.3.2/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml:141: specfied ==> specified data/paleomix-1.3.2/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml:149: partioned ==> partitioned data/paleomix-1.3.2/paleomix/resources/rscripts/zonkey/tinytree.r:281: Convinience ==> Convenience data/paleomix-1.3.2/paleomix/resources/rscripts/zonkey/treemix.r:576: Insufficent ==> Insufficient data/paleomix-1.3.2/paleomix/tools/validate_fastq.py:69: AMBIGIOUS ==> AMBIGUOUS data/paleomix-1.3.2/paleomix/tools/vcf_to_fasta.py:23: Creats ==> Creates data/paleomix-1.3.2/tests/atomiccmd_test/command_test.py:161: nd ==> and, 2nd data/paleomix-1.3.2/tests/atomiccmd_test/command_test.py:165: nd ==> and, 2nd data/paleomix-1.3.2/tests/atomiccmd_test/command_test.py:537: Proccess ==> Process data/paleomix-1.3.2/tests/common_tests/fileutils_test.py:207: expection ==> exception data/paleomix-1.3.2/tests/common_tests/fileutils_test.py:222: premission ==> permission data/paleomix-1.3.2/tests/common_tests/fileutils_test.py:224: premission ==> permission data/paleomix-1.3.2/tests/common_tests/utilities_test.py:249: Convertion ==> Conversion data/paleomix-1.3.2/tests/common_tests/formats_tests/fastq_test.py:257: AMBIGIOUS ==> AMBIGUOUS