.coveragerc
CHANGELOG.md
CONTRIBUTING.md
COPYING.txt
MANIFEST.in
Makefile
PULL_REQUEST_TEMPLATE.md
README.rst
RELEASE.md
REVIEWING.md
asv.conf.json
checklist.py
setup.cfg
setup.py
assets/.no.gif
assets/horizontal_powered_by.png
assets/horizontal_powered_by.svg
assets/logo-inverted.svg
assets/logo.png
assets/logo.svg
assets/logo_and_powered.pdf
assets/vertical_powered_by.png
assets/vertical_powered_by.svg
benchmarks/__init__.py
benchmarks/benchmarks.py
ci/conda_requirements.txt
ci/matplotlibrc
ci/pip_requirements.txt
doc/Makefile
doc/README.md
doc/source/alignment.rst
doc/source/conf.py
doc/source/diversity.rst
doc/source/index.rst
doc/source/io.rst
doc/source/metadata.rst
doc/source/sequence.rst
doc/source/stats.rst
doc/source/tree.rst
doc/source/util.rst
doc/source/workflow.rst
doc/source/_static/copybutton.js
doc/source/_static/style.css
doc/source/_templates/layout.html
doc/source/_templates/autosummary/attribute.rst
doc/source/_templates/autosummary/class.rst
doc/source/_templates/autosummary/method.rst
doc/source/_templates/autosummary/module.rst
doc/source/development/coding_guidelines.rst
doc/source/development/new_module.rst
doc/source/user/api_stability.rst
doc/source/user/assets/api-lifecycle.png
ipynbs/presentations/2014.05.13-jairideout/README.md
ipynbs/presentations/2014.05.13-jairideout/dm.txt
ipynbs/presentations/2014.05.13-jairideout/map.txt
ipynbs/presentations/2014.05.13-jairideout/scikit-bio presentation.ipynb
ipynbs/presentations/2014.05.13-jairideout/smalldm.txt
ipynbs/presentations/2014.05.13-jairideout/style.css
ipynbs/presentations/2014.05.13-jairideout/talktools.py
ipynbs/presentations/2014.07.09-gregcaporaso/caporaso-scipy2014.ipynb
ipynbs/presentations/2014.07.09-gregcaporaso/code-deletion-pr.png
ipynbs/presentations/2014.07.09-gregcaporaso/code-sprint-1.jpg
ipynbs/presentations/2014.07.09-gregcaporaso/code-sprint-2.jpg
ipynbs/presentations/2014.07.09-gregcaporaso/custom.css
ipynbs/presentations/2014.07.09-gregcaporaso/iab-example.png
ipynbs/presentations/2014.07.09-gregcaporaso/logo.png
ipynbs/presentations/2014.07.09-gregcaporaso/qiime-cites.png
ipynbs/presentations/2014.07.09-gregcaporaso/skbio-alignment-docs.png
ipynbs/presentations/2014.07.09-gregcaporaso/skbio-bdiv-docs.png
ipynbs/presentations/2014.07.09-gregcaporaso/skbio-contributors.png
ipynbs/presentations/2014.07.09-gregcaporaso/skbio-docs.png
ipynbs/presentations/2014.07.09-gregcaporaso/skbio-timeline.png
ipynbs/presentations/2014.07.09-gregcaporaso/skbio.png
ipynbs/presentations/2014.07.09-gregcaporaso/style.css
ipynbs/presentations/2014.07.09-gregcaporaso/talktools.py
licenses/bx_python.txt
licenses/fastq-example-files-readme.txt
licenses/flask.txt
licenses/ipython.txt
licenses/nb-slideshow-template.txt
licenses/qiita.txt
licenses/scikit-learn.txt
licenses/scipy.txt
licenses/sphinx-bootstrap-theme.txt
licenses/ssw.txt
licenses/verman.txt
scikit_bio.egg-info/PKG-INFO
scikit_bio.egg-info/SOURCES.txt
scikit_bio.egg-info/dependency_links.txt
scikit_bio.egg-info/requires.txt
scikit_bio.egg-info/top_level.txt
skbio/__init__.py
skbio/_base.py
skbio/test.py
skbio/workflow.py
skbio/alignment/__init__.py
skbio/alignment/_indexing.py
skbio/alignment/_pairwise.py
skbio/alignment/_repr.py
skbio/alignment/_ssw_wrapper.c
skbio/alignment/_ssw_wrapper.pyx
skbio/alignment/_tabular_msa.py
skbio/alignment/_lib/__init__.py
skbio/alignment/_lib/ssw.c
skbio/alignment/_lib/ssw.h
skbio/alignment/tests/__init__.py
skbio/alignment/tests/test_pairwise.py
skbio/alignment/tests/test_ssw.py
skbio/alignment/tests/test_tabular_msa.py
skbio/diversity/__init__.py
skbio/diversity/_block.py
skbio/diversity/_driver.py
skbio/diversity/_phylogenetic.c
skbio/diversity/_phylogenetic.pyx
skbio/diversity/_util.py
skbio/diversity/alpha/__init__.py
skbio/diversity/alpha/_ace.py
skbio/diversity/alpha/_base.py
skbio/diversity/alpha/_chao1.py
skbio/diversity/alpha/_faith_pd.py
skbio/diversity/alpha/_gini.py
skbio/diversity/alpha/_lladser.py
skbio/diversity/alpha/tests/__init__.py
skbio/diversity/alpha/tests/test_ace.py
skbio/diversity/alpha/tests/test_base.py
skbio/diversity/alpha/tests/test_chao1.py
skbio/diversity/alpha/tests/test_faith_pd.py
skbio/diversity/alpha/tests/test_gini.py
skbio/diversity/alpha/tests/test_lladser.py
skbio/diversity/alpha/tests/data/qiime-191-tt/README.md
skbio/diversity/alpha/tests/data/qiime-191-tt/faith-pd.txt
skbio/diversity/alpha/tests/data/qiime-191-tt/otu-table.tsv
skbio/diversity/alpha/tests/data/qiime-191-tt/tree.nwk
skbio/diversity/beta/__init__.py
skbio/diversity/beta/_unifrac.py
skbio/diversity/beta/tests/__init__.py
skbio/diversity/beta/tests/test_unifrac.py
skbio/diversity/beta/tests/data/qiime-191-tt/README.md
skbio/diversity/beta/tests/data/qiime-191-tt/otu-table.tsv
skbio/diversity/beta/tests/data/qiime-191-tt/tree.nwk
skbio/diversity/beta/tests/data/qiime-191-tt/unweighted_unifrac_dm.txt
skbio/diversity/beta/tests/data/qiime-191-tt/weighted_normalized_unifrac_dm.txt
skbio/diversity/beta/tests/data/qiime-191-tt/weighted_unifrac_dm.txt
skbio/diversity/tests/__init__.py
skbio/diversity/tests/test_block.py
skbio/diversity/tests/test_driver.py
skbio/diversity/tests/test_util.py
skbio/io/__init__.py
skbio/io/_exception.py
skbio/io/_fileobject.py
skbio/io/_iosources.py
skbio/io/_warning.py
skbio/io/registry.py
skbio/io/util.py
skbio/io/format/__init__.py
skbio/io/format/_base.py
skbio/io/format/_blast.py
skbio/io/format/_sequence_feature_vocabulary.py
skbio/io/format/blast6.py
skbio/io/format/blast7.py
skbio/io/format/clustal.py
skbio/io/format/embl.py
skbio/io/format/emptyfile.py
skbio/io/format/fasta.py
skbio/io/format/fastq.py
skbio/io/format/genbank.py
skbio/io/format/gff3.py
skbio/io/format/lsmat.py
skbio/io/format/newick.py
skbio/io/format/ordination.py
skbio/io/format/phylip.py
skbio/io/format/qseq.py
skbio/io/format/stockholm.py
skbio/io/format/tests/__init__.py
skbio/io/format/tests/test_base.py
skbio/io/format/tests/test_blast6.py
skbio/io/format/tests/test_blast7.py
skbio/io/format/tests/test_clustal.py
skbio/io/format/tests/test_embl.py
skbio/io/format/tests/test_emptyfile.py
skbio/io/format/tests/test_fasta.py
skbio/io/format/tests/test_fastq.py
skbio/io/format/tests/test_genbank.py
skbio/io/format/tests/test_gff3.py
skbio/io/format/tests/test_lsmat.py
skbio/io/format/tests/test_newick.py
skbio/io/format/tests/test_ordination.py
skbio/io/format/tests/test_phylip.py
skbio/io/format/tests/test_qseq.py
skbio/io/format/tests/test_sequence_feature_vocabulary.py
skbio/io/format/tests/test_stockholm.py
skbio/io/format/tests/data/blast6_custom_minimal
skbio/io/format/tests/data/blast6_custom_mixed_nans
skbio/io/format/tests/data/blast6_custom_multi_line
skbio/io/format/tests/data/blast6_custom_single_line
skbio/io/format/tests/data/blast6_default_multi_line
skbio/io/format/tests/data/blast6_default_single_line
skbio/io/format/tests/data/blast6_invalid_column_types
skbio/io/format/tests/data/blast6_invalid_number_of_columns
skbio/io/format/tests/data/blast6_invalid_type_in_column
skbio/io/format/tests/data/blast7_custom_minimal
skbio/io/format/tests/data/blast7_custom_mixed_nans
skbio/io/format/tests/data/blast7_custom_multi_line
skbio/io/format/tests/data/blast7_custom_single_line
skbio/io/format/tests/data/blast7_default_multi_line
skbio/io/format/tests/data/blast7_default_single_line
skbio/io/format/tests/data/blast7_invalid_differing_fields
skbio/io/format/tests/data/blast7_invalid_for_sniffer
skbio/io/format/tests/data/blast7_invalid_for_sniffer_2
skbio/io/format/tests/data/blast7_invalid_gibberish
skbio/io/format/tests/data/blast7_invalid_no_data
skbio/io/format/tests/data/blast7_invalid_too_many_columns
skbio/io/format/tests/data/blast7_invalid_unrecognized_field
skbio/io/format/tests/data/embl_constructed
skbio/io/format/tests/data/embl_feature_level_record
skbio/io/format/tests/data/embl_feature_level_record_no_FT
skbio/io/format/tests/data/embl_multi_records
skbio/io/format/tests/data/embl_single_record
skbio/io/format/tests/data/embl_single_record_lower
skbio/io/format/tests/data/embl_single_record_simple
skbio/io/format/tests/data/embl_single_record_upper
skbio/io/format/tests/data/embl_uniprot_record
skbio/io/format/tests/data/embl_w_beginning_whitespace
skbio/io/format/tests/data/empty
skbio/io/format/tests/data/error_diff_ids.fastq
skbio/io/format/tests/data/error_double_qual.fastq
skbio/io/format/tests/data/error_double_seq.fastq
skbio/io/format/tests/data/error_long_qual.fastq
skbio/io/format/tests/data/error_no_qual.fastq
skbio/io/format/tests/data/error_qual_del.fastq
skbio/io/format/tests/data/error_qual_escape.fastq
skbio/io/format/tests/data/error_qual_null.fastq
skbio/io/format/tests/data/error_qual_space.fastq
skbio/io/format/tests/data/error_qual_tab.fastq
skbio/io/format/tests/data/error_qual_unit_sep.fastq
skbio/io/format/tests/data/error_qual_vtab.fastq
skbio/io/format/tests/data/error_short_qual.fastq
skbio/io/format/tests/data/error_spaces.fastq
skbio/io/format/tests/data/error_tabs.fastq
skbio/io/format/tests/data/error_trunc_at_plus.fastq
skbio/io/format/tests/data/error_trunc_at_qual.fastq
skbio/io/format/tests/data/error_trunc_at_seq.fastq
skbio/io/format/tests/data/error_trunc_in_plus.fastq
skbio/io/format/tests/data/error_trunc_in_qual.fastq
skbio/io/format/tests/data/error_trunc_in_seq.fastq
skbio/io/format/tests/data/error_trunc_in_title.fastq
skbio/io/format/tests/data/fasta_10_seqs
skbio/io/format/tests/data/fasta_3_seqs_defaults
skbio/io/format/tests/data/fasta_3_seqs_non_defaults
skbio/io/format/tests/data/fasta_5_blanks_start_of_file
skbio/io/format/tests/data/fasta_5_ws_lines_start_of_file
skbio/io/format/tests/data/fasta_6_blanks_start_of_file
skbio/io/format/tests/data/fasta_6_ws_lines_start_of_file
skbio/io/format/tests/data/fasta_blank_lines_between_records
skbio/io/format/tests/data/fasta_blanks_end_of_file
skbio/io/format/tests/data/fasta_description_newline_replacement_empty_str
skbio/io/format/tests/data/fasta_description_newline_replacement_multi_char
skbio/io/format/tests/data/fasta_description_newline_replacement_none
skbio/io/format/tests/data/fasta_id_whitespace_replacement_empty_str
skbio/io/format/tests/data/fasta_id_whitespace_replacement_multi_char
skbio/io/format/tests/data/fasta_id_whitespace_replacement_none
skbio/io/format/tests/data/fasta_invalid_after_10_seqs
skbio/io/format/tests/data/fasta_invalid_blank_line_after_header
skbio/io/format/tests/data/fasta_invalid_blank_line_within_sequence
skbio/io/format/tests/data/fasta_invalid_blank_sequence
skbio/io/format/tests/data/fasta_invalid_legacy_format
skbio/io/format/tests/data/fasta_invalid_missing_header
skbio/io/format/tests/data/fasta_invalid_missing_seq_data_first
skbio/io/format/tests/data/fasta_invalid_missing_seq_data_last
skbio/io/format/tests/data/fasta_invalid_missing_seq_data_middle
skbio/io/format/tests/data/fasta_invalid_whitespace_line_after_header
skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence
skbio/io/format/tests/data/fasta_invalid_whitespace_only_sequence
skbio/io/format/tests/data/fasta_max_width_1
skbio/io/format/tests/data/fasta_max_width_5
skbio/io/format/tests/data/fasta_mixed_qual_scores
skbio/io/format/tests/data/fasta_multi_seq
skbio/io/format/tests/data/fasta_multi_seq_roundtrip
skbio/io/format/tests/data/fasta_prot_seqs_odd_labels
skbio/io/format/tests/data/fasta_single_bio_seq_defaults
skbio/io/format/tests/data/fasta_single_bio_seq_non_defaults
skbio/io/format/tests/data/fasta_single_dna_seq_defaults
skbio/io/format/tests/data/fasta_single_dna_seq_non_defaults
skbio/io/format/tests/data/fasta_single_prot_seq_defaults
skbio/io/format/tests/data/fasta_single_prot_seq_non_defaults
skbio/io/format/tests/data/fasta_single_rna_seq_defaults
skbio/io/format/tests/data/fasta_single_rna_seq_non_defaults
skbio/io/format/tests/data/fasta_single_seq
skbio/io/format/tests/data/fasta_tabular_msa_different_type
skbio/io/format/tests/data/fasta_ws_lines_between_records
skbio/io/format/tests/data/fasta_ws_lines_end_of_file
skbio/io/format/tests/data/fastq_5_blanks_start_of_file
skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file
skbio/io/format/tests/data/fastq_blank_lines
skbio/io/format/tests/data/fastq_invalid_blank_after_header
skbio/io/format/tests/data/fastq_invalid_blank_after_plus
skbio/io/format/tests/data/fastq_invalid_blank_after_seq
skbio/io/format/tests/data/fastq_invalid_blank_in_seq_at_symbol
skbio/io/format/tests/data/fastq_invalid_blank_within_qual
skbio/io/format/tests/data/fastq_invalid_blank_within_seq
skbio/io/format/tests/data/fastq_invalid_missing_header
skbio/io/format/tests/data/fastq_invalid_missing_seq_data
skbio/io/format/tests/data/fastq_invalid_ws_line_after_header
skbio/io/format/tests/data/fastq_invalid_ws_line_after_plus
skbio/io/format/tests/data/fastq_invalid_ws_line_after_seq
skbio/io/format/tests/data/fastq_invalid_ws_line_within_qual
skbio/io/format/tests/data/fastq_invalid_ws_line_within_seq
skbio/io/format/tests/data/fastq_multi_blank_between_records
skbio/io/format/tests/data/fastq_multi_blank_end_of_file
skbio/io/format/tests/data/fastq_multi_blank_start_of_file
skbio/io/format/tests/data/fastq_multi_seq_sanger
skbio/io/format/tests/data/fastq_multi_whitespace_stripping
skbio/io/format/tests/data/fastq_multi_ws_lines_between_records
skbio/io/format/tests/data/fastq_multi_ws_lines_end_of_file
skbio/io/format/tests/data/fastq_multi_ws_lines_start_of_file
skbio/io/format/tests/data/fastq_single_seq_illumina1.3
skbio/io/format/tests/data/fastq_single_seq_illumina1.8
skbio/io/format/tests/data/fastq_whitespace_only_lines
skbio/io/format/tests/data/fastq_wrapping_as_illumina_no_description
skbio/io/format/tests/data/fastq_wrapping_as_sanger_no_description
skbio/io/format/tests/data/fastq_wrapping_original_sanger_no_description
skbio/io/format/tests/data/fastq_writer_illumina1.3_defaults
skbio/io/format/tests/data/fastq_writer_sanger_defaults
skbio/io/format/tests/data/fastq_writer_sanger_non_defaults
skbio/io/format/tests/data/genbank_5_blanks_start_of_file
skbio/io/format/tests/data/genbank_6_blanks_start_of_file
skbio/io/format/tests/data/genbank_missing_locus_name
skbio/io/format/tests/data/genbank_multi_records
skbio/io/format/tests/data/genbank_single_record
skbio/io/format/tests/data/genbank_single_record_lower
skbio/io/format/tests/data/genbank_single_record_upper
skbio/io/format/tests/data/genbank_w_beginning_whitespace
skbio/io/format/tests/data/gff3_bad_missing_directive
skbio/io/format/tests/data/gff3_bad_wrong_columns
skbio/io/format/tests/data/gff3_dna
skbio/io/format/tests/data/gff3_multi_record
skbio/io/format/tests/data/gff3_single_record
skbio/io/format/tests/data/illumina_full_range_as_illumina.fastq
skbio/io/format/tests/data/illumina_full_range_as_sanger.fastq
skbio/io/format/tests/data/illumina_full_range_original_illumina.fastq
skbio/io/format/tests/data/legacy9_and_blast7_default
skbio/io/format/tests/data/legacy9_invalid_differing_fields
skbio/io/format/tests/data/legacy9_invalid_too_many_columns
skbio/io/format/tests/data/legacy9_mixed_nans
skbio/io/format/tests/data/legacy9_multi_line
skbio/io/format/tests/data/legacy9_single_line
skbio/io/format/tests/data/longreads_as_illumina.fastq
skbio/io/format/tests/data/longreads_as_sanger.fastq
skbio/io/format/tests/data/longreads_original_sanger.fastq
skbio/io/format/tests/data/misc_dna_as_illumina.fastq
skbio/io/format/tests/data/misc_dna_as_sanger.fastq
skbio/io/format/tests/data/misc_dna_original_sanger.fastq
skbio/io/format/tests/data/misc_rna_as_illumina.fastq
skbio/io/format/tests/data/misc_rna_as_sanger.fastq
skbio/io/format/tests/data/misc_rna_original_sanger.fastq
skbio/io/format/tests/data/ordination_L&L_CA_data_scores
skbio/io/format/tests/data/ordination_PCoA_sample_data_3_scores
skbio/io/format/tests/data/ordination_error1
skbio/io/format/tests/data/ordination_error10
skbio/io/format/tests/data/ordination_error11
skbio/io/format/tests/data/ordination_error12
skbio/io/format/tests/data/ordination_error13
skbio/io/format/tests/data/ordination_error14
skbio/io/format/tests/data/ordination_error15
skbio/io/format/tests/data/ordination_error16
skbio/io/format/tests/data/ordination_error17
skbio/io/format/tests/data/ordination_error18
skbio/io/format/tests/data/ordination_error19
skbio/io/format/tests/data/ordination_error2
skbio/io/format/tests/data/ordination_error20
skbio/io/format/tests/data/ordination_error21
skbio/io/format/tests/data/ordination_error22
skbio/io/format/tests/data/ordination_error23
skbio/io/format/tests/data/ordination_error24
skbio/io/format/tests/data/ordination_error3
skbio/io/format/tests/data/ordination_error4
skbio/io/format/tests/data/ordination_error5
skbio/io/format/tests/data/ordination_error6
skbio/io/format/tests/data/ordination_error7
skbio/io/format/tests/data/ordination_error8
skbio/io/format/tests/data/ordination_error9
skbio/io/format/tests/data/ordination_example2_scores
skbio/io/format/tests/data/ordination_example3_scores
skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site
skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site_constraints
skbio/io/format/tests/data/ordination_exp_Ordination_CCA_species
skbio/io/format/tests/data/ordination_exp_Ordination_PCoA_site
skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site
skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site_constraints
skbio/io/format/tests/data/ordination_exp_Ordination_RDA_species
skbio/io/format/tests/data/phylip_dna_3_seqs
skbio/io/format/tests/data/phylip_invalid_empty_line_after_header
skbio/io/format/tests/data/phylip_invalid_empty_line_before_header
skbio/io/format/tests/data/phylip_invalid_empty_line_between_seqs
skbio/io/format/tests/data/phylip_invalid_header_too_long
skbio/io/format/tests/data/phylip_invalid_header_too_short
skbio/io/format/tests/data/phylip_invalid_no_header
skbio/io/format/tests/data/phylip_invalid_seq_too_long
skbio/io/format/tests/data/phylip_invalid_seq_too_short
skbio/io/format/tests/data/phylip_invalid_too_few_seqs
skbio/io/format/tests/data/phylip_invalid_too_many_seqs
skbio/io/format/tests/data/phylip_invalid_zero_seq_len
skbio/io/format/tests/data/phylip_invalid_zero_seqs
skbio/io/format/tests/data/phylip_single_seq_long
skbio/io/format/tests/data/phylip_single_seq_short
skbio/io/format/tests/data/phylip_two_chunks
skbio/io/format/tests/data/phylip_variable_length_ids
skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs
skbio/io/format/tests/data/phylip_whitespace_in_header_1
skbio/io/format/tests/data/phylip_whitespace_in_header_2
skbio/io/format/tests/data/phylip_whitespace_in_header_3
skbio/io/format/tests/data/qseq_invalid_filter
skbio/io/format/tests/data/qseq_invalid_lane
skbio/io/format/tests/data/qseq_invalid_read
skbio/io/format/tests/data/qseq_invalid_tile
skbio/io/format/tests/data/qseq_invalid_x
skbio/io/format/tests/data/qseq_invalid_y
skbio/io/format/tests/data/qseq_multi_seq_illumina1.3
skbio/io/format/tests/data/qseq_single_seq_sanger
skbio/io/format/tests/data/qual_2_seqs_defaults
skbio/io/format/tests/data/qual_3_seqs_defaults
skbio/io/format/tests/data/qual_3_seqs_defaults_desc_mismatch
skbio/io/format/tests/data/qual_3_seqs_defaults_extra
skbio/io/format/tests/data/qual_3_seqs_defaults_id_mismatch
skbio/io/format/tests/data/qual_3_seqs_defaults_length_mismatch
skbio/io/format/tests/data/qual_3_seqs_non_defaults
skbio/io/format/tests/data/qual_5_blanks_start_of_file
skbio/io/format/tests/data/qual_5_ws_lines_start_of_file
skbio/io/format/tests/data/qual_6_blanks_start_of_file
skbio/io/format/tests/data/qual_6_ws_lines_start_of_file
skbio/io/format/tests/data/qual_blank_lines_between_records
skbio/io/format/tests/data/qual_blanks_end_of_file

skbio/io/format/tests/data/qual_invalid_blank_sequence
skbio/io/format/tests/data/qual_invalid_legacy_format
skbio/io/format/tests/data/qual_invalid_missing_header
skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first
skbio/io/format/tests/data/qual_invalid_missing_qual_scores_last
skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle
skbio/io/format/tests/data/qual_invalid_qual_scores_float
skbio/io/format/tests/data/qual_invalid_qual_scores_negative
skbio/io/format/tests/data/qual_invalid_qual_scores_over_255
skbio/io/format/tests/data/qual_invalid_qual_scores_string
skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq
skbio/io/format/tests/data/qual_invalid_whitespace_only_sequence
skbio/io/format/tests/data/qual_invalid_ws_line_after_header
skbio/io/format/tests/data/qual_max_width_1
skbio/io/format/tests/data/qual_max_width_5
skbio/io/format/tests/data/qual_multi_seq
skbio/io/format/tests/data/qual_multi_seq_roundtrip
skbio/io/format/tests/data/qual_prot_seqs_odd_labels
skbio/io/format/tests/data/qual_single_bio_seq_non_defaults
skbio/io/format/tests/data/qual_single_dna_seq_non_defaults
skbio/io/format/tests/data/qual_single_nuc_seq_non_defaults
skbio/io/format/tests/data/qual_single_prot_seq_non_defaults
skbio/io/format/tests/data/qual_single_rna_seq_non_defaults
skbio/io/format/tests/data/qual_single_seq
skbio/io/format/tests/data/qual_tabular_msa_different_type
skbio/io/format/tests/data/qual_ws_lines_between_records
skbio/io/format/tests/data/qual_ws_lines_end_of_file
skbio/io/format/tests/data/sanger_full_range_as_illumina.fastq
skbio/io/format/tests/data/sanger_full_range_as_sanger.fastq
skbio/io/format/tests/data/sanger_full_range_original_sanger.fastq
skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq
skbio/io/format/tests/data/stockholm_all_data_types
skbio/io/format/tests/data/stockholm_blank_lines
skbio/io/format/tests/data/stockholm_data_only
skbio/io/format/tests/data/stockholm_different_padding
skbio/io/format/tests/data/stockholm_differing_gc_data_length
skbio/io/format/tests/data/stockholm_differing_gr_data_length
skbio/io/format/tests/data/stockholm_differing_seq_lengths
skbio/io/format/tests/data/stockholm_duplicate_gc
skbio/io/format/tests/data/stockholm_duplicate_gr
skbio/io/format/tests/data/stockholm_duplicate_sequence_names
skbio/io/format/tests/data/stockholm_duplicate_tree_ids
skbio/io/format/tests/data/stockholm_extensive
skbio/io/format/tests/data/stockholm_extensive_mixed
skbio/io/format/tests/data/stockholm_invalid_data_type
skbio/io/format/tests/data/stockholm_invalid_nonexistent_gr
skbio/io/format/tests/data/stockholm_invalid_nonexistent_gs
skbio/io/format/tests/data/stockholm_malformed_data_line
skbio/io/format/tests/data/stockholm_malformed_gc_line
skbio/io/format/tests/data/stockholm_malformed_gf_line
skbio/io/format/tests/data/stockholm_malformed_gr_line
skbio/io/format/tests/data/stockholm_malformed_gs_line
skbio/io/format/tests/data/stockholm_metadata_only
skbio/io/format/tests/data/stockholm_minimal
skbio/io/format/tests/data/stockholm_missing_footer
skbio/io/format/tests/data/stockholm_missing_header
skbio/io/format/tests/data/stockholm_missing_reference_items
skbio/io/format/tests/data/stockholm_missing_rn_tag
skbio/io/format/tests/data/stockholm_multi_line_tree_no_id
skbio/io/format/tests/data/stockholm_multi_line_tree_with_id
skbio/io/format/tests/data/stockholm_multiple_msa
skbio/io/format/tests/data/stockholm_multiple_multi_line_trees
skbio/io/format/tests/data/stockholm_multiple_references
skbio/io/format/tests/data/stockholm_multiple_trees
skbio/io/format/tests/data/stockholm_no_data
skbio/io/format/tests/data/stockholm_nonstring_labels
skbio/io/format/tests/data/stockholm_rna
skbio/io/format/tests/data/stockholm_runon_gf_no_whitespace
skbio/io/format/tests/data/stockholm_runon_gf_with_whitespace
skbio/io/format/tests/data/stockholm_runon_gs_no_whitespace
skbio/io/format/tests/data/stockholm_runon_gs_with_whitespace
skbio/io/format/tests/data/stockholm_runon_references
skbio/io/format/tests/data/stockholm_runon_references_mixed
skbio/io/format/tests/data/stockholm_single_reference
skbio/io/format/tests/data/stockholm_single_tree_with_id
skbio/io/format/tests/data/stockholm_single_tree_without_id
skbio/io/format/tests/data/stockholm_two_of_each_metadata
skbio/io/format/tests/data/stockholm_whitespace_only_lines
skbio/io/format/tests/data/tsv_10_fields
skbio/io/format/tests/data/tsv_8_fields
skbio/io/format/tests/data/whitespace_only
skbio/io/format/tests/data/wrapping_as_illumina.fastq
skbio/io/format/tests/data/wrapping_as_sanger.fastq
skbio/io/format/tests/data/wrapping_original_sanger.fastq
skbio/io/tests/__init__.py
skbio/io/tests/test_iosources.py
skbio/io/tests/test_registry.py
skbio/io/tests/test_util.py
skbio/io/tests/data/big5_file
skbio/io/tests/data/big5_file.bz2
skbio/io/tests/data/big5_file.gz
skbio/io/tests/data/example_file
skbio/io/tests/data/example_file.bz2
skbio/io/tests/data/example_file.gz
skbio/io/tests/data/real_file
skbio/io/tests/data/real_file_2
skbio/metadata/__init__.py
skbio/metadata/_intersection.c
skbio/metadata/_intersection.pyx
skbio/metadata/_interval.py
skbio/metadata/_mixin.py
skbio/metadata/_repr.py
skbio/metadata/_testing.py
skbio/metadata/tests/__init__.py
skbio/metadata/tests/test_intersection.py
skbio/metadata/tests/test_interval.py
skbio/metadata/tests/test_mixin.py
skbio/sequence/__init__.py
skbio/sequence/_dna.py
skbio/sequence/_genetic_code.py
skbio/sequence/_grammared_sequence.py
skbio/sequence/_nucleotide_mixin.py
skbio/sequence/_protein.py
skbio/sequence/_repr.py
skbio/sequence/_rna.py
skbio/sequence/_sequence.py
skbio/sequence/distance.py
skbio/sequence/tests/__init__.py
skbio/sequence/tests/test_distance.py
skbio/sequence/tests/test_dna.py
skbio/sequence/tests/test_genetic_code.py
skbio/sequence/tests/test_grammared_sequence.py
skbio/sequence/tests/test_nucleotide_sequences.py
skbio/sequence/tests/test_protein.py
skbio/sequence/tests/test_rna.py
skbio/sequence/tests/test_sequence.py
skbio/stats/__init__.py
skbio/stats/__subsample.c
skbio/stats/__subsample.pyx
skbio/stats/_misc.py
skbio/stats/_subsample.py
skbio/stats/composition.py
skbio/stats/gradient.py
skbio/stats/power.py
skbio/stats/distance/__init__.py
skbio/stats/distance/_anosim.py
skbio/stats/distance/_base.py
skbio/stats/distance/_bioenv.py
skbio/stats/distance/_mantel.py
skbio/stats/distance/_permanova.py
skbio/stats/distance/tests/__init__.py
skbio/stats/distance/tests/test_anosim.py
skbio/stats/distance/tests/test_base.py
skbio/stats/distance/tests/test_bioenv.py
skbio/stats/distance/tests/test_mantel.py
skbio/stats/distance/tests/test_permanova.py
skbio/stats/distance/tests/data/bioenv_df_vegan.txt
skbio/stats/distance/tests/data/bioenv_dm_vegan.txt
skbio/stats/distance/tests/data/bioenv_exp_results_vegan.txt
skbio/stats/distance/tests/data/df.txt
skbio/stats/distance/tests/data/df_extra_column.txt
skbio/stats/distance/tests/data/dm.txt
skbio/stats/distance/tests/data/dm2.txt
skbio/stats/distance/tests/data/dm3.txt
skbio/stats/distance/tests/data/dm4.txt
skbio/stats/distance/tests/data/dm_reordered.txt
skbio/stats/distance/tests/data/exp_results.txt
skbio/stats/distance/tests/data/exp_results_different_column_order.txt
skbio/stats/distance/tests/data/exp_results_single_column.txt
skbio/stats/distance/tests/data/mantel_env_dm_vegan.txt
skbio/stats/distance/tests/data/mantel_veg_dm_vegan.txt
skbio/stats/distance/tests/data/pwmantel_exp_results_all_dms.txt
skbio/stats/distance/tests/data/pwmantel_exp_results_dm_dm2.txt
skbio/stats/distance/tests/data/pwmantel_exp_results_duplicate_dms.txt
skbio/stats/distance/tests/data/pwmantel_exp_results_minimal.txt
skbio/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt
skbio/stats/distance/tests/data/pwmantel_exp_results_na_p_value.txt
skbio/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt
skbio/stats/evolve/__init__.py
skbio/stats/evolve/_hommola.py
skbio/stats/evolve/tests/__init__.py
skbio/stats/evolve/tests/test_hommola.py
skbio/stats/ordination/__init__.py
skbio/stats/ordination/_canonical_correspondence_analysis.py
skbio/stats/ordination/_correspondence_analysis.py
skbio/stats/ordination/_ordination_results.py
skbio/stats/ordination/_principal_coordinate_analysis.py
skbio/stats/ordination/_redundancy_analysis.py
skbio/stats/ordination/_utils.py
skbio/stats/ordination/tests/__init__.py
skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py
skbio/stats/ordination/tests/test_correspondence_analysis.py
skbio/stats/ordination/tests/test_ordination_results.py
skbio/stats/ordination/tests/test_principal_coordinate_analysis.py
skbio/stats/ordination/tests/test_redundancy_analysis.py
skbio/stats/ordination/tests/test_util.py
skbio/stats/ordination/tests/data/L&L_CA_data
skbio/stats/ordination/tests/data/PCoA_sample_data
skbio/stats/ordination/tests/data/PCoA_sample_data_2
skbio/stats/ordination/tests/data/PCoA_sample_data_3
skbio/stats/ordination/tests/data/example2_X
skbio/stats/ordination/tests/data/example2_Y
skbio/stats/ordination/tests/data/example2_biplot_scaling1
skbio/stats/ordination/tests/data/example2_biplot_scaling2
skbio/stats/ordination/tests/data/example2_sample_constraints_scaling1
skbio/stats/ordination/tests/data/example2_sample_constraints_scaling2
skbio/stats/ordination/tests/data/example2_site_scaling1_from_vegan
skbio/stats/ordination/tests/data/example2_site_scaling2_from_vegan
skbio/stats/ordination/tests/data/example2_species_scaling1_from_vegan
skbio/stats/ordination/tests/data/example2_species_scaling2_from_vegan
skbio/stats/ordination/tests/data/example3_X
skbio/stats/ordination/tests/data/example3_Y
skbio/stats/ordination/tests/data/example3_biplot_scaling1
skbio/stats/ordination/tests/data/example3_biplot_scaling2
skbio/stats/ordination/tests/data/example3_sample_constraints_scaling1
skbio/stats/ordination/tests/data/example3_sample_constraints_scaling2
skbio/stats/ordination/tests/data/example3_site_scaling1_from_vegan
skbio/stats/ordination/tests/data/example3_site_scaling2_from_vegan
skbio/stats/ordination/tests/data/example3_species_scaling1_from_vegan
skbio/stats/ordination/tests/data/example3_species_scaling2_from_vegan
skbio/stats/ordination/tests/data/exp_PCoAEigenResults_site
skbio/stats/ordination/tests/data/exp_PCoAzeros_site
skbio/stats/ordination/tests/data/vare_rda_biplot_from_vegan.csv
skbio/stats/ordination/tests/data/vare_rda_constraints_from_vegan.csv
skbio/stats/ordination/tests/data/vare_rda_eigvals_from_vegan.csv
skbio/stats/ordination/tests/data/vare_rda_propexpl_from_vegan.csv
skbio/stats/ordination/tests/data/vare_rda_sites_from_vegan.csv
skbio/stats/ordination/tests/data/vare_rda_species_from_vegan.csv
skbio/stats/ordination/tests/data/varechem.csv
skbio/stats/ordination/tests/data/varespec.csv
skbio/stats/tests/__init__.py
skbio/stats/tests/test_composition.py
skbio/stats/tests/test_gradient.py
skbio/stats/tests/test_misc.py
skbio/stats/tests/test_power.py
skbio/stats/tests/test_subsample.py
skbio/stats/tests/data/cr_data_out
skbio/stats/tests/data/cr_data_raw
skbio/stats/tests/data/cr_no_data_out
skbio/stats/tests/data/cr_no_data_raw
skbio/stats/tests/data/gr_w_msg_out
skbio/stats/tests/data/gr_w_msg_raw
skbio/stats/tests/data/gr_wo_msg_out
skbio/stats/tests/data/gr_wo_msg_raw
skbio/stats/tests/data/vr_out
skbio/stats/tests/data/vr_raw
skbio/stats/tests/data/vr_real_out
skbio/stats/tests/data/vr_real_raw
skbio/tests/__init__.py
skbio/tests/test_base.py
skbio/tests/test_workflow.py
skbio/tree/__init__.py
skbio/tree/_exception.py
skbio/tree/_majority_rule.py
skbio/tree/_nj.py
skbio/tree/_tree.py
skbio/tree/tests/__init__.py
skbio/tree/tests/test_majority_rule.py
skbio/tree/tests/test_nj.py
skbio/tree/tests/test_tree.py
skbio/util/__init__.py
skbio/util/_decorator.py
skbio/util/_exception.py
skbio/util/_misc.py
skbio/util/_testing.py
skbio/util/_warning.py
skbio/util/tests/__init__.py
skbio/util/tests/test_decorator.py
skbio/util/tests/test_misc.py
skbio/util/tests/test_testing.py