python-cogent_1.5.3-10_amd64.deb


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Description

python-cogent - framework for genomic biology

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe amd64
Package name: python-cogent
Package version: 1.5.3
Package release: 10
Package architecture: amd64
Package type: deb
Installed size: 4.80 KB
Download size: 917.63 KB
Official Mirror: archive.ubuntu.com
PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: * controlling third-party applications, * devising workflows; querying databases, * conducting novel probabilistic analyses of biological sequence evolution, and * generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.

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    Download

    Source package: python-cogent

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install python-cogent deb package:
      # sudo apt-get install python-cogent

    Files

    • /usr/lib/python2.7/dist-packages/cogent-1.5.3.egg-info
    • /usr/lib/python2.7/dist-packages/cogent/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/align/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/align/_compare.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/align/_pairwise_pogs.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/align/_pairwise_seqs.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/align/algorithm.py
    • /usr/lib/python2.7/dist-packages/cogent/align/align.py
    • /usr/lib/python2.7/dist-packages/cogent/align/dp_calculation.py
    • /usr/lib/python2.7/dist-packages/cogent/align/indel_model.py
    • /usr/lib/python2.7/dist-packages/cogent/align/indel_positions.py
    • /usr/lib/python2.7/dist-packages/cogent/align/pairwise.py
    • /usr/lib/python2.7/dist-packages/cogent/align/progressive.py
    • /usr/lib/python2.7/dist-packages/cogent/align/pycompare.py
    • /usr/lib/python2.7/dist-packages/cogent/align/traceback.py
    • /usr/lib/python2.7/dist-packages/cogent/align/weights/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/align/weights/methods.py
    • /usr/lib/python2.7/dist-packages/cogent/align/weights/util.py
    • /usr/lib/python2.7/dist-packages/cogent/app/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/app/blast.py
    • /usr/lib/python2.7/dist-packages/cogent/app/blat.py
    • /usr/lib/python2.7/dist-packages/cogent/app/bwa.py
    • /usr/lib/python2.7/dist-packages/cogent/app/carnac.py
    • /usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py
    • /usr/lib/python2.7/dist-packages/cogent/app/clearcut.py
    • /usr/lib/python2.7/dist-packages/cogent/app/clustalw.py
    • /usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py
    • /usr/lib/python2.7/dist-packages/cogent/app/comrna.py
    • /usr/lib/python2.7/dist-packages/cogent/app/consan.py
    • /usr/lib/python2.7/dist-packages/cogent/app/contrafold.py
    • /usr/lib/python2.7/dist-packages/cogent/app/cove.py
    • /usr/lib/python2.7/dist-packages/cogent/app/dialign.py
    • /usr/lib/python2.7/dist-packages/cogent/app/dotur.py
    • /usr/lib/python2.7/dist-packages/cogent/app/dynalign.py
    • /usr/lib/python2.7/dist-packages/cogent/app/fasttree.py
    • /usr/lib/python2.7/dist-packages/cogent/app/fasttree_v1.py
    • /usr/lib/python2.7/dist-packages/cogent/app/foldalign.py
    • /usr/lib/python2.7/dist-packages/cogent/app/formatdb.py
    • /usr/lib/python2.7/dist-packages/cogent/app/gctmpca.py
    • /usr/lib/python2.7/dist-packages/cogent/app/guppy.py
    • /usr/lib/python2.7/dist-packages/cogent/app/ilm.py
    • /usr/lib/python2.7/dist-packages/cogent/app/infernal.py
    • /usr/lib/python2.7/dist-packages/cogent/app/knetfold.py
    • /usr/lib/python2.7/dist-packages/cogent/app/mafft.py
    • /usr/lib/python2.7/dist-packages/cogent/app/mfold.py
    • /usr/lib/python2.7/dist-packages/cogent/app/mothur.py
    • /usr/lib/python2.7/dist-packages/cogent/app/msms.py
    • /usr/lib/python2.7/dist-packages/cogent/app/muscle.py
    • /usr/lib/python2.7/dist-packages/cogent/app/muscle_v38.py
    • /usr/lib/python2.7/dist-packages/cogent/app/nupack.py
    • /usr/lib/python2.7/dist-packages/cogent/app/parameters.py
    • /usr/lib/python2.7/dist-packages/cogent/app/parsinsert.py
    • /usr/lib/python2.7/dist-packages/cogent/app/pfold.py
    • /usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py
    • /usr/lib/python2.7/dist-packages/cogent/app/pplacer.py
    • /usr/lib/python2.7/dist-packages/cogent/app/raxml.py
    • /usr/lib/python2.7/dist-packages/cogent/app/raxml_v730.py
    • /usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier.py
    • /usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier20.py
    • /usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py
    • /usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py
    • /usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py
    • /usr/lib/python2.7/dist-packages/cogent/app/rnaview.py
    • /usr/lib/python2.7/dist-packages/cogent/app/rtax.py
    • /usr/lib/python2.7/dist-packages/cogent/app/sfffile.py
    • /usr/lib/python2.7/dist-packages/cogent/app/sffinfo.py
    • /usr/lib/python2.7/dist-packages/cogent/app/sfold.py
    • /usr/lib/python2.7/dist-packages/cogent/app/stride.py
    • /usr/lib/python2.7/dist-packages/cogent/app/uclust.py
    • /usr/lib/python2.7/dist-packages/cogent/app/unafold.py
    • /usr/lib/python2.7/dist-packages/cogent/app/usearch.py
    • /usr/lib/python2.7/dist-packages/cogent/app/util.py
    • /usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py
    • /usr/lib/python2.7/dist-packages/cogent/cluster/UPGMA.py
    • /usr/lib/python2.7/dist-packages/cogent/cluster/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/cluster/approximate_mds.py
    • /usr/lib/python2.7/dist-packages/cogent/cluster/goodness_of_fit.py
    • /usr/lib/python2.7/dist-packages/cogent/cluster/metric_scaling.py
    • /usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py
    • /usr/lib/python2.7/dist-packages/cogent/cluster/procrustes.py
    • /usr/lib/python2.7/dist-packages/cogent/core/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/core/alignment.py
    • /usr/lib/python2.7/dist-packages/cogent/core/alphabet.py
    • /usr/lib/python2.7/dist-packages/cogent/core/annotation.py
    • /usr/lib/python2.7/dist-packages/cogent/core/bitvector.py
    • /usr/lib/python2.7/dist-packages/cogent/core/entity.py
    • /usr/lib/python2.7/dist-packages/cogent/core/genetic_code.py
    • /usr/lib/python2.7/dist-packages/cogent/core/info.py
    • /usr/lib/python2.7/dist-packages/cogent/core/location.py
    • /usr/lib/python2.7/dist-packages/cogent/core/moltype.py
    • /usr/lib/python2.7/dist-packages/cogent/core/profile.py
    • /usr/lib/python2.7/dist-packages/cogent/core/sequence.py
    • /usr/lib/python2.7/dist-packages/cogent/core/tree.py
    • /usr/lib/python2.7/dist-packages/cogent/core/usage.py
    • /usr/lib/python2.7/dist-packages/cogent/data/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/data/energy_params.py
    • /usr/lib/python2.7/dist-packages/cogent/data/ligand_properties.py
    • /usr/lib/python2.7/dist-packages/cogent/data/molecular_weight.py
    • /usr/lib/python2.7/dist-packages/cogent/data/nucleic_properties.py
    • /usr/lib/python2.7/dist-packages/cogent/data/protein_properties.py
    • /usr/lib/python2.7/dist-packages/cogent/db/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ncbi.py
    • /usr/lib/python2.7/dist-packages/cogent/db/pdb.py
    • /usr/lib/python2.7/dist-packages/cogent/db/rfam.py
    • /usr/lib/python2.7/dist-packages/cogent/db/util.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/assembly.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/compara.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/database.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/feature_level.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/genome.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/host.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/name.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/region.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/related_region.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/sequence.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/species.py
    • /usr/lib/python2.7/dist-packages/cogent/db/ensembl/util.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/codon_usage.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/compatibility.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/dendrogram.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/dinuc.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/distribution_plots.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/dotplot.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/fancy_arrow.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/legend.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/linear.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/multivariate_plot.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py
    • /usr/lib/python2.7/dist-packages/cogent/draw/util.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/_likelihood_tree.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/evolve/_pairwise_distance.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/evolve/_solved_models.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/evolve/best_likelihood.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/bootstrap.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/discrete_markov.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_calculation.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_function.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_tree.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/models.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/motif_prob_model.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/pairwise_distance.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/parameter_controller.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/predicate.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/simulate.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/solved_models.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py
    • /usr/lib/python2.7/dist-packages/cogent/evolve/substitution_model.py
    • /usr/lib/python2.7/dist-packages/cogent/format/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/format/alignment.py
    • /usr/lib/python2.7/dist-packages/cogent/format/bedgraph.py
    • /usr/lib/python2.7/dist-packages/cogent/format/clustal.py
    • /usr/lib/python2.7/dist-packages/cogent/format/fasta.py
    • /usr/lib/python2.7/dist-packages/cogent/format/mage.py
    • /usr/lib/python2.7/dist-packages/cogent/format/motif.py
    • /usr/lib/python2.7/dist-packages/cogent/format/nexus.py
    • /usr/lib/python2.7/dist-packages/cogent/format/pdb.py
    • /usr/lib/python2.7/dist-packages/cogent/format/pdb_color.py
    • /usr/lib/python2.7/dist-packages/cogent/format/phylip.py
    • /usr/lib/python2.7/dist-packages/cogent/format/rna_struct.py
    • /usr/lib/python2.7/dist-packages/cogent/format/stockholm.py
    • /usr/lib/python2.7/dist-packages/cogent/format/structure.py
    • /usr/lib/python2.7/dist-packages/cogent/format/table.py
    • /usr/lib/python2.7/dist-packages/cogent/format/text_tree.py
    • /usr/lib/python2.7/dist-packages/cogent/format/xyzrn.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/_period.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/fit_function.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/function_optimisation.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/geometry.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/markov.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/matrix_exponentiation.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/matrix_logarithm.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/optimisers.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/period.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimisers.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/simannealingoptimiser.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/solve.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/svd.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/matrix/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/matrix/distance.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/spatial/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/spatial/ckd3.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/alpha_diversity.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/distribution.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/histogram.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/information_criteria.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/jackknife.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/kendall.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/ks.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/period.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/rarefaction.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/special.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/get_by_cai.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/unifrac/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_tree.py
    • /usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_unifrac.py
    • /usr/lib/python2.7/dist-packages/cogent/motif/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/motif/k_word.py
    • /usr/lib/python2.7/dist-packages/cogent/motif/util.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/aaindex.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/agilent_microarray.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/binary_sff.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/blast.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/blast_xml.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/bowtie.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/bpseq.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/carnac.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/cigar.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/clustal.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/cmfinder.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/column.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/comrna.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/consan.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/contrafold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/cove.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/ct.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/cut.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/cutg.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/dialign.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/dotur.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/dynalign.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/ebi.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/fasta.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/fastq.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/flowgram.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/flowgram_parser.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/foldalign.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/gbseq.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/gcg.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/genbank.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/gff.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/gibbs.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/greengenes.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/illumina_sequence.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/ilm.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/infernal.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/kegg_fasta.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/kegg_pos.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/knetfold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/locuslink.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/macsim.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/mage.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/meme.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/mfold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/mothur.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/msms.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/ncbi_taxonomy.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/newick.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/nexus.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/nupack.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/paml.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/paml_matrix.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/pdb.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/pfold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/phylip.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/pknotsrg.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/psl.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rdb.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/record.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/record_finder.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rfam.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rna_fold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rna_plot.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rnaalifold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rnaforester.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/rnaview.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/sequence.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/sfold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/sprinzl.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/stockholm.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/stride.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/structure.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/table.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/tinyseq.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/tree.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/tree_xml.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/unafold.py
    • /usr/lib/python2.7/dist-packages/cogent/parse/unigene.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/consensus.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/distance.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/least_squares.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/maximum_likelihood.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/nj.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/tree_collection.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/tree_space.py
    • /usr/lib/python2.7/dist-packages/cogent/phylo/util.py
    • /usr/lib/python2.7/dist-packages/cogent/recalculation/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/recalculation/calculation.py
    • /usr/lib/python2.7/dist-packages/cogent/recalculation/definition.py
    • /usr/lib/python2.7/dist-packages/cogent/recalculation/scope.py
    • /usr/lib/python2.7/dist-packages/cogent/recalculation/setting.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/birth_death.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/microarray.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/randomization.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/searchpath.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/sequence_generators.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/tree.py
    • /usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/_asa.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/struct/_contact.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/cogent/struct/annotation.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/asa.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/contact.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/dihedral.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/knots.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/manipulation.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/pairs_util.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/rna2d.py
    • /usr/lib/python2.7/dist-packages/cogent/struct/selection.py
    • /usr/lib/python2.7/dist-packages/cogent/util/__init__.py
    • /usr/lib/python2.7/dist-packages/cogent/util/array.py
    • /usr/lib/python2.7/dist-packages/cogent/util/checkpointing.py
    • /usr/lib/python2.7/dist-packages/cogent/util/datatypes.py
    • /usr/lib/python2.7/dist-packages/cogent/util/dict2d.py
    • /usr/lib/python2.7/dist-packages/cogent/util/dict_array.py
    • /usr/lib/python2.7/dist-packages/cogent/util/misc.py
    • /usr/lib/python2.7/dist-packages/cogent/util/modules.py
    • /usr/lib/python2.7/dist-packages/cogent/util/option_parsing.py
    • /usr/lib/python2.7/dist-packages/cogent/util/organizer.py
    • /usr/lib/python2.7/dist-packages/cogent/util/parallel.py
    • /usr/lib/python2.7/dist-packages/cogent/util/progress_display.py
    • /usr/lib/python2.7/dist-packages/cogent/util/recode_alignment.py
    • /usr/lib/python2.7/dist-packages/cogent/util/table.py
    • /usr/lib/python2.7/dist-packages/cogent/util/terminal.py
    • /usr/lib/python2.7/dist-packages/cogent/util/transform.py
    • /usr/lib/python2.7/dist-packages/cogent/util/trie.py
    • /usr/lib/python2.7/dist-packages/cogent/util/unit_test.py
    • /usr/lib/python2.7/dist-packages/cogent/util/update_version.py
    • /usr/lib/python2.7/dist-packages/cogent/util/warning.py
    • /usr/share/doc/python-cogent/README.Debian
    • /usr/share/doc/python-cogent/changelog.Debian.gz
    • /usr/share/doc/python-cogent/copyright

    Changelog

    2015-12-30 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-10) unstable; urgency=medium * mothur does not exist on s390x * exclude test failed on i386 also on kfreebsd-i386

    2015-12-26 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-9) unstable; urgency=medium * Different autobuilder seems to fail on different tests - exclude another two tests on i386

    2015-12-25 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-8) unstable; urgency=medium * Ignore some more test issues only on ppc64

    2015-12-24 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-7) unstable; urgency=medium * Ignore a few test failures on certain architectures to at least document the problem debian/README.source was created

    2015-12-23 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-6) unstable; urgency=medium * Also deal with raxml that only exists on [any-amd64 any-i386]

    2015-12-23 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-5) unstable; urgency=medium * Also deal with infernal that only exists on [any-amd64 any-i386]

    2015-12-23 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-4) unstable; urgency=medium * Build-Depends: bwa [any-amd64] and exclude bwa tests for other architectures Closes: #808799 * Really activate tests but only those that are known to pass. All failed tests excluded for the moment - more detailed investigation is needed * Drop debug package in favour of automatically generated one * Add hint about tests to README.Debian.

    2015-05-21 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-3) unstable; urgency=medium * cme fix dpkg-control * Priority: optional (except for *-dbg) * DEP5 * debian/watch: Adapted to Github * DEP3 * README.source removed since redundant * cme fix dpkg-control * Adapt to the naming scheme of cd-hit inside Debian Closes: #730515 * Switch from python-support to pybuild Closes: #786073

    2014-04-25 - Tim Booth <tbooth@ceh.ac.uk> python-cogent (1.5.3-2biolinux1) trusty; urgency=low * Allow use of newer cd-hit that doesn't leave a tmp file Note - the tests still fail as output is different, but this is a quick fix. * Also make the script compatible with our parsinsert package * Add suggests dep on both of these * Rebuild for Trusty

    2013-05-30 - Andreas Tille <tille@debian.org> python-cogent (1.5.3-2) unstable; urgency=low * debian/rules: Add -f option to rm statements to not fail if files to be remove do not exist Closes: #710339

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