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