README
setup.py
cogent/__init__.py
cogent.egg-info/PKG-INFO
cogent.egg-info/SOURCES.txt
cogent.egg-info/dependency_links.txt
cogent.egg-info/requires.txt
cogent.egg-info/top_level.txt
cogent/align/__init__.py
cogent/align/_compare.c
cogent/align/_pairwise_pogs.c
cogent/align/_pairwise_seqs.c
cogent/align/algorithm.py
cogent/align/align.py
cogent/align/dp_calculation.py
cogent/align/indel_model.py
cogent/align/indel_positions.py
cogent/align/pairwise.py
cogent/align/progressive.py
cogent/align/pycompare.py
cogent/align/traceback.py
cogent/align/weights/__init__.py
cogent/align/weights/methods.py
cogent/align/weights/util.py
cogent/app/__init__.py
cogent/app/blast.py
cogent/app/blat.py
cogent/app/bwa.py
cogent/app/carnac.py
cogent/app/cd_hit.py
cogent/app/cdbfasta.py
cogent/app/clearcut.py
cogent/app/clustalw.py
cogent/app/cmfinder.py
cogent/app/comrna.py
cogent/app/consan.py
cogent/app/contrafold.py
cogent/app/cove.py
cogent/app/dialign.py
cogent/app/dotur.py
cogent/app/dynalign.py
cogent/app/fastq_join.py
cogent/app/fasttree.py
cogent/app/fasttree_v1.py
cogent/app/flash.py
cogent/app/foldalign.py
cogent/app/formatdb.py
cogent/app/gctmpca.py
cogent/app/guppy.py
cogent/app/ilm.py
cogent/app/infernal.py
cogent/app/knetfold.py
cogent/app/mafft.py
cogent/app/mfold.py
cogent/app/mothur.py
cogent/app/msms.py
cogent/app/muscle.py
cogent/app/muscle_v38.py
cogent/app/nupack.py
cogent/app/pandaseq.py
cogent/app/parameters.py
cogent/app/parsinsert.py
cogent/app/pfold.py
cogent/app/pknotsrg.py
cogent/app/pplacer.py
cogent/app/raxml.py
cogent/app/raxml_v730.py
cogent/app/rdp_classifier.py
cogent/app/rdp_classifier20.py
cogent/app/rnaalifold.py
cogent/app/rnaforester.py
cogent/app/rnashapes.py
cogent/app/rnaview.py
cogent/app/rtax.py
cogent/app/seqprep.py
cogent/app/sfffile.py
cogent/app/sffinfo.py
cogent/app/sfold.py
cogent/app/stride.py
cogent/app/uclust.py
cogent/app/unafold.py
cogent/app/usearch.py
cogent/app/util.py
cogent/app/vienna_package.py
cogent/cluster/UPGMA.py
cogent/cluster/__init__.py
cogent/cluster/approximate_mds.py
cogent/cluster/goodness_of_fit.py
cogent/cluster/metric_scaling.py
cogent/cluster/nmds.py
cogent/cluster/procrustes.py
cogent/core/__init__.py
cogent/core/alignment.py
cogent/core/alphabet.py
cogent/core/annotation.py
cogent/core/bitvector.py
cogent/core/entity.py
cogent/core/genetic_code.py
cogent/core/info.py
cogent/core/location.py
cogent/core/moltype.py
cogent/core/profile.py
cogent/core/sequence.py
cogent/core/tree.py
cogent/core/usage.py
cogent/data/__init__.py
cogent/data/energy_params.py
cogent/data/ligand_properties.py
cogent/data/molecular_weight.py
cogent/data/nucleic_properties.py
cogent/data/protein_properties.py
cogent/db/__init__.py
cogent/db/ncbi.py
cogent/db/pdb.py
cogent/db/rfam.py
cogent/db/util.py
cogent/db/ensembl/__init__.py
cogent/db/ensembl/assembly.py
cogent/db/ensembl/compara.py
cogent/db/ensembl/database.py
cogent/db/ensembl/feature_level.py
cogent/db/ensembl/genome.py
cogent/db/ensembl/host.py
cogent/db/ensembl/name.py
cogent/db/ensembl/region.py
cogent/db/ensembl/related_region.py
cogent/db/ensembl/sequence.py
cogent/db/ensembl/species.py
cogent/db/ensembl/util.py
cogent/draw/__init__.py
cogent/draw/arrow_rates.py
cogent/draw/codon_usage.py
cogent/draw/compatibility.py
cogent/draw/dendrogram.py
cogent/draw/dinuc.py
cogent/draw/distribution_plots.py
cogent/draw/dotplot.py
cogent/draw/fancy_arrow.py
cogent/draw/legend.py
cogent/draw/linear.py
cogent/draw/multivariate_plot.py
cogent/draw/rlg2mpl.py
cogent/draw/util.py
cogent/evolve/__init__.py
cogent/evolve/_likelihood_tree.c
cogent/evolve/_pairwise_distance.c
cogent/evolve/_solved_models.c
cogent/evolve/best_likelihood.py
cogent/evolve/bootstrap.py
cogent/evolve/coevolution.py
cogent/evolve/discrete_markov.py
cogent/evolve/likelihood_calculation.py
cogent/evolve/likelihood_function.py
cogent/evolve/likelihood_tree.py
cogent/evolve/models.py
cogent/evolve/motif_prob_model.py
cogent/evolve/pairwise_distance.py
cogent/evolve/parameter_controller.py
cogent/evolve/predicate.py
cogent/evolve/simulate.py
cogent/evolve/solved_models.py
cogent/evolve/substitution_calculation.py
cogent/evolve/substitution_model.py
cogent/format/__init__.py
cogent/format/alignment.py
cogent/format/bedgraph.py
cogent/format/clustal.py
cogent/format/fasta.py
cogent/format/mage.py
cogent/format/motif.py
cogent/format/nexus.py
cogent/format/pdb.py
cogent/format/pdb_color.py
cogent/format/phylip.py
cogent/format/rna_struct.py
cogent/format/stockholm.py
cogent/format/structure.py
cogent/format/table.py
cogent/format/text_tree.py
cogent/format/xyzrn.py
cogent/maths/__init__.py
cogent/maths/_period.c
cogent/maths/distance_transform.py
cogent/maths/fit_function.py
cogent/maths/function_optimisation.py
cogent/maths/geometry.py
cogent/maths/markov.py
cogent/maths/matrix_exponential_integration.py
cogent/maths/matrix_exponentiation.py
cogent/maths/matrix_logarithm.py
cogent/maths/optimisers.py
cogent/maths/period.py
cogent/maths/scipy_optimisers.py
cogent/maths/scipy_optimize.py
cogent/maths/simannealingoptimiser.py
cogent/maths/solve.py
cogent/maths/svd.py
cogent/maths/matrix/__init__.py
cogent/maths/matrix/distance.py
cogent/maths/spatial/__init__.py
cogent/maths/spatial/ckd3.c
cogent/maths/stats/__init__.py
cogent/maths/stats/alpha_diversity.py
cogent/maths/stats/distribution.py
cogent/maths/stats/histogram.py
cogent/maths/stats/information_criteria.py
cogent/maths/stats/jackknife.py
cogent/maths/stats/kendall.py
cogent/maths/stats/ks.py
cogent/maths/stats/period.py
cogent/maths/stats/rarefaction.py
cogent/maths/stats/special.py
cogent/maths/stats/test.py
cogent/maths/stats/util.py
cogent/maths/stats/cai/__init__.py
cogent/maths/stats/cai/adaptor.py
cogent/maths/stats/cai/get_by_cai.py
cogent/maths/stats/cai/util.py
cogent/maths/unifrac/__init__.py
cogent/maths/unifrac/fast_tree.py
cogent/maths/unifrac/fast_unifrac.py
cogent/motif/__init__.py
cogent/motif/k_word.py
cogent/motif/util.py
cogent/parse/__init__.py
cogent/parse/aaindex.py
cogent/parse/agilent_microarray.py
cogent/parse/binary_sff.py
cogent/parse/blast.py
cogent/parse/blast_xml.py
cogent/parse/bowtie.py
cogent/parse/bpseq.py
cogent/parse/carnac.py
cogent/parse/cigar.py
cogent/parse/clustal.py
cogent/parse/cmfinder.py
cogent/parse/column.py
cogent/parse/comrna.py
cogent/parse/consan.py
cogent/parse/contrafold.py
cogent/parse/cove.py
cogent/parse/ct.py
cogent/parse/cut.py
cogent/parse/cutg.py
cogent/parse/dialign.py
cogent/parse/dotur.py
cogent/parse/dynalign.py
cogent/parse/ebi.py
cogent/parse/fasta.py
cogent/parse/fastq.py
cogent/parse/flowgram.py
cogent/parse/flowgram_collection.py
cogent/parse/flowgram_parser.py
cogent/parse/foldalign.py
cogent/parse/gbseq.py
cogent/parse/gcg.py
cogent/parse/genbank.py
cogent/parse/gff.py
cogent/parse/gibbs.py
cogent/parse/greengenes.py
cogent/parse/hmmscan.py
cogent/parse/illumina_sequence.py
cogent/parse/ilm.py
cogent/parse/infernal.py
cogent/parse/kegg_fasta.py
cogent/parse/kegg_ko.py
cogent/parse/kegg_pos.py
cogent/parse/kegg_taxonomy.py
cogent/parse/knetfold.py
cogent/parse/locuslink.py
cogent/parse/macsim.py
cogent/parse/mage.py
cogent/parse/meme.py
cogent/parse/mfold.py
cogent/parse/mothur.py
cogent/parse/msms.py
cogent/parse/ncbi_taxonomy.py
cogent/parse/newick.py
cogent/parse/nexus.py
cogent/parse/nupack.py
cogent/parse/paml.py
cogent/parse/paml_matrix.py
cogent/parse/pdb.py
cogent/parse/pfold.py
cogent/parse/phylip.py
cogent/parse/pknotsrg.py
cogent/parse/psl.py
cogent/parse/rdb.py
cogent/parse/record.py
cogent/parse/record_finder.py
cogent/parse/rfam.py
cogent/parse/rna_fold.py
cogent/parse/rna_plot.py
cogent/parse/rnaalifold.py
cogent/parse/rnaforester.py
cogent/parse/rnashapes.py
cogent/parse/rnaview.py
cogent/parse/sequence.py
cogent/parse/sfold.py
cogent/parse/sprinzl.py
cogent/parse/stockholm.py
cogent/parse/stride.py
cogent/parse/structure.py
cogent/parse/table.py
cogent/parse/tinyseq.py
cogent/parse/tree.py
cogent/parse/tree_xml.py
cogent/parse/unafold.py
cogent/parse/unigene.py
cogent/phylo/__init__.py
cogent/phylo/consensus.py
cogent/phylo/distance.py
cogent/phylo/least_squares.py
cogent/phylo/maximum_likelihood.py
cogent/phylo/nj.py
cogent/phylo/tree_collection.py
cogent/phylo/tree_space.py
cogent/phylo/util.py
cogent/recalculation/__init__.py
cogent/recalculation/calculation.py
cogent/recalculation/definition.py
cogent/recalculation/scope.py
cogent/recalculation/setting.py
cogent/seqsim/__init__.py
cogent/seqsim/analysis.py
cogent/seqsim/birth_death.py
cogent/seqsim/markov.py
cogent/seqsim/microarray.py
cogent/seqsim/microarray_normalize.py
cogent/seqsim/randomization.py
cogent/seqsim/searchpath.py
cogent/seqsim/sequence_generators.py
cogent/seqsim/tree.py
cogent/seqsim/usage.py
cogent/struct/__init__.py
cogent/struct/_asa.c
cogent/struct/_contact.c
cogent/struct/annotation.py
cogent/struct/asa.py
cogent/struct/contact.py
cogent/struct/dihedral.py
cogent/struct/knots.py
cogent/struct/manipulation.py
cogent/struct/pairs_util.py
cogent/struct/rna2d.py
cogent/struct/selection.py
cogent/util/__init__.py
cogent/util/array.py
cogent/util/checkpointing.py
cogent/util/datatypes.py
cogent/util/dict2d.py
cogent/util/dict_array.py
cogent/util/misc.py
cogent/util/modules.py
cogent/util/option_parsing.py
cogent/util/organizer.py
cogent/util/parallel.py
cogent/util/progress_display.py
cogent/util/recode_alignment.py
cogent/util/table.py
cogent/util/terminal.py
cogent/util/transform.py
cogent/util/trie.py
cogent/util/unit_test.py
cogent/util/update_version.py
cogent/util/warning.py