CITATION.txt
LICENSE
MANIFEST.in
README.rst
THANKS.rst
VERSION
ez_setup.py
setup.py
doc/.buildinfo
doc/ETE.pdf
doc/about.html
doc/genindex.html
doc/index.html
doc/objects.inv
doc/py-modindex.html
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doc/_downloads/nexml_annotated_trees.py
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ete3/__init__.py
ete3/_ph.py
ete3/citation.py
ete3/utils.py
ete3/version.py
ete3.egg-info/PKG-INFO
ete3.egg-info/SOURCES.txt
ete3.egg-info/dependency_links.txt
ete3.egg-info/entry_points.txt
ete3.egg-info/top_level.txt
ete3/clustering/__init__.py
ete3/clustering/clustertree.py
ete3/clustering/clustvalidation.py
ete3/coretype/__init__.py
ete3/coretype/arraytable.py
ete3/coretype/seqgroup.py
ete3/coretype/tree.py
ete3/evol/__init__.py
ete3/evol/control.py
ete3/evol/evoltree.py
ete3/evol/model.py
ete3/evol/utils.py
ete3/evol/parser/__init__.py
ete3/evol/parser/codemlparser.py
ete3/evol/parser/slrparser.py
ete3/ncbi_taxonomy/__init__.py
ete3/ncbi_taxonomy/ncbiquery.py
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ete3/nexml/_nexml_tree.py
ete3/orthoxml/__init__.py
ete3/orthoxml/_orthoxml.py
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ete3/parser/fasta.py
ete3/parser/newick.py
ete3/parser/paml.py
ete3/parser/phylip.py
ete3/parser/text_arraytable.py
ete3/phylo/__init__.py
ete3/phylo/evolevents.py
ete3/phylo/phylotree.py
ete3/phylo/reconciliation.py
ete3/phylo/spoverlap.py
ete3/phylomedb/__init__.py
ete3/phylomedb/phylomeDB.py
ete3/phylomedb/phylomeDB3.py
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ete3/tools/ete_build.py
ete3/tools/ete_compare.py
ete3/tools/ete_evol.py
ete3/tools/ete_expand.py
ete3/tools/ete_extract.py
ete3/tools/ete_generate.py
ete3/tools/ete_maptrees.py
ete3/tools/ete_mod.py
ete3/tools/ete_ncbiquery.py
ete3/tools/ete_split.py
ete3/tools/ete_upgrade_tools.py
ete3/tools/ete_view.py
ete3/tools/utils.py
ete3/tools/ete_build_lib/__init__.py
ete3/tools/ete_build_lib/apps.py
ete3/tools/ete_build_lib/configcheck.py
ete3/tools/ete_build_lib/configobj.py
ete3/tools/ete_build_lib/curses_gui.py
ete3/tools/ete_build_lib/db.py
ete3/tools/ete_build_lib/errors.py
ete3/tools/ete_build_lib/getch.py
ete3/tools/ete_build_lib/interface.py
ete3/tools/ete_build_lib/logger.py
ete3/tools/ete_build_lib/master_job.py
ete3/tools/ete_build_lib/master_task.py
ete3/tools/ete_build_lib/ordereddict.py
ete3/tools/ete_build_lib/scheduler.py
ete3/tools/ete_build_lib/seqio.py
ete3/tools/ete_build_lib/sge.py
ete3/tools/ete_build_lib/utils.py
ete3/tools/ete_build_lib/validate.py
ete3/tools/ete_build_lib/visualize.py
ete3/tools/ete_build_lib/task/__init__.py
ete3/tools/ete_build_lib/task/clustalo.py
ete3/tools/ete_build_lib/task/cog_creator.py
ete3/tools/ete_build_lib/task/cog_selector.py
ete3/tools/ete_build_lib/task/concat_alg.py
ete3/tools/ete_build_lib/task/dialigntx.py
ete3/tools/ete_build_lib/task/dummyalg.py
ete3/tools/ete_build_lib/task/dummytree.py
ete3/tools/ete_build_lib/task/fasttree.py
ete3/tools/ete_build_lib/task/iqtree.py
ete3/tools/ete_build_lib/task/jmodeltest.py
ete3/tools/ete_build_lib/task/mafft.py
ete3/tools/ete_build_lib/task/merger.py
ete3/tools/ete_build_lib/task/meta_aligner.py
ete3/tools/ete_build_lib/task/msf.py
ete3/tools/ete_build_lib/task/muscle.py
ete3/tools/ete_build_lib/task/phyml.py
ete3/tools/ete_build_lib/task/pmodeltest.py
ete3/tools/ete_build_lib/task/prottest.py
ete3/tools/ete_build_lib/task/prottest2.py
ete3/tools/ete_build_lib/task/raxml.py
ete3/tools/ete_build_lib/task/tcoffee.py
ete3/tools/ete_build_lib/task/trimal.py
ete3/tools/ete_build_lib/task/uhire.py
ete3/tools/ete_build_lib/workflow/__init__.py
ete3/tools/ete_build_lib/workflow/common.py
ete3/tools/ete_build_lib/workflow/genetree.py
ete3/tools/ete_build_lib/workflow/supermatrix.py
ete3/treeview/__init__.py
ete3/treeview/_about.py
ete3/treeview/_mainwindow.py
ete3/treeview/_open_newick.py
ete3/treeview/_search_dialog.py
ete3/treeview/_show_codeml.py
ete3/treeview/_show_newick.py
ete3/treeview/about.ui
ete3/treeview/clean_search.png
ete3/treeview/drawer.py
ete3/treeview/ete_icon.png
ete3/treeview/ete_logo.png
ete3/treeview/ete_qt4app.ui
ete3/treeview/ete_resources.qrc
ete3/treeview/ete_resources_rc.py
ete3/treeview/export_pdf.png
ete3/treeview/faces.py
ete3/treeview/fileopen.png
ete3/treeview/filesave.png
ete3/treeview/fit_region.png
ete3/treeview/fit_tree.png
ete3/treeview/force_topo.png
ete3/treeview/image_properties.ui
ete3/treeview/layouts.py
ete3/treeview/main.py
ete3/treeview/node_gui_actions.py
ete3/treeview/open_newick.ui
ete3/treeview/qt.py
ete3/treeview/qt4_circular_render.py
ete3/treeview/qt4_compile_resources.sh
ete3/treeview/qt4_face_render.py
ete3/treeview/qt4_gui.py
ete3/treeview/qt4_rect_render.py
ete3/treeview/qt4_render.py
ete3/treeview/search.png
ete3/treeview/search_dialog.ui
ete3/treeview/show_dist.png
ete3/treeview/show_names.png
ete3/treeview/show_newick.png
ete3/treeview/show_newick.ui
ete3/treeview/show_support.png
ete3/treeview/svg_colors.py
ete3/treeview/templates.py
ete3/treeview/x_expand.png
ete3/treeview/x_reduce.png
ete3/treeview/y_expand.png
ete3/treeview/y_reduce.png
ete3/treeview/zoom_in.png
ete3/treeview/zoom_out.png
ete3/webplugin/__init__.py
ete3/webplugin/webapp.py
examples/clustering/bubbles_validation.py
examples/clustering/cluster_visualization.py
examples/clustering/clustering_tree.py
examples/clustering/diauxic.array
examples/clustering/diauxic.nw
examples/evol/1_freeratio.py
examples/evol/2_sites_model.py
examples/evol/3_branchsite_test.py
examples/evol/4_branch_models.py
examples/evol/5_branchsite_cladetest.py
examples/evol/6_ancestral_sequence.py
examples/evol/7_slr.py
examples/evol/README
examples/evol/measuring_evolution_trees.py
examples/evol/test_hist.py
examples/evol/test_protamine.py
examples/evol/data/CladeModelCD/ECP_EDN_15.fasta
examples/evol/data/CladeModelCD/ECP_EDN_15.nw
examples/evol/data/L_example/alignment_L_measuring_evol.fasta
examples/evol/data/L_example/measuring_L_tree.nw
examples/evol/data/S_example/alignment_S_measuring_evol.fasta
examples/evol/data/S_example/measuring_S_tree.nw
examples/evol/data/S_example/paml/M1/2NG.dN
examples/evol/data/S_example/paml/M1/2NG.dS
examples/evol/data/S_example/paml/M1/2NG.t
examples/evol/data/S_example/paml/M1/4fold.nuc
examples/evol/data/S_example/paml/M1/algn
examples/evol/data/S_example/paml/M1/lnf
examples/evol/data/S_example/paml/M1/out
examples/evol/data/S_example/paml/M1/rst
examples/evol/data/S_example/paml/M1/rst1
examples/evol/data/S_example/paml/M1/rub
examples/evol/data/S_example/paml/M1/tmp.ctl
examples/evol/data/S_example/paml/M1/tree
examples/evol/data/S_example/paml/M2/2NG.dN
examples/evol/data/S_example/paml/M2/2NG.dS
examples/evol/data/S_example/paml/M2/2NG.t
examples/evol/data/S_example/paml/M2/4fold.nuc
examples/evol/data/S_example/paml/M2/algn
examples/evol/data/S_example/paml/M2/lnf
examples/evol/data/S_example/paml/M2/out
examples/evol/data/S_example/paml/M2/rst
examples/evol/data/S_example/paml/M2/rst1
examples/evol/data/S_example/paml/M2/rub
examples/evol/data/S_example/paml/M2/tmp.ctl
examples/evol/data/S_example/paml/M2/tree
examples/evol/data/S_example/paml/bsA/2NG.dN
examples/evol/data/S_example/paml/bsA/2NG.dS
examples/evol/data/S_example/paml/bsA/2NG.t
examples/evol/data/S_example/paml/bsA/4fold.nuc
examples/evol/data/S_example/paml/bsA/algn
examples/evol/data/S_example/paml/bsA/lnf
examples/evol/data/S_example/paml/bsA/out
examples/evol/data/S_example/paml/bsA/rst
examples/evol/data/S_example/paml/bsA/rst1
examples/evol/data/S_example/paml/bsA/rub
examples/evol/data/S_example/paml/bsA/tmp.ctl
examples/evol/data/S_example/paml/bsA/tree
examples/evol/data/S_example/paml/bsA1/2NG.dN
examples/evol/data/S_example/paml/bsA1/2NG.dS
examples/evol/data/S_example/paml/bsA1/2NG.t
examples/evol/data/S_example/paml/bsA1/4fold.nuc
examples/evol/data/S_example/paml/bsA1/algn
examples/evol/data/S_example/paml/bsA1/lnf
examples/evol/data/S_example/paml/bsA1/out
examples/evol/data/S_example/paml/bsA1/rst
examples/evol/data/S_example/paml/bsA1/rst1
examples/evol/data/S_example/paml/bsA1/rub
examples/evol/data/S_example/paml/bsA1/tmp.ctl
examples/evol/data/S_example/paml/bsA1/tree
examples/evol/data/S_example/paml/fb/2NG.dN
examples/evol/data/S_example/paml/fb/2NG.dS
examples/evol/data/S_example/paml/fb/2NG.t
examples/evol/data/S_example/paml/fb/4fold.nuc
examples/evol/data/S_example/paml/fb/algn
examples/evol/data/S_example/paml/fb/lnf
examples/evol/data/S_example/paml/fb/out
examples/evol/data/S_example/paml/fb/rst
examples/evol/data/S_example/paml/fb/rst1
examples/evol/data/S_example/paml/fb/rub
examples/evol/data/S_example/paml/fb/tmp.ctl
examples/evol/data/S_example/paml/fb/tree
examples/evol/data/protamine/PRM1/alignments.fasta_ali
examples/evol/data/protamine/PRM1/tree.nw
examples/evol/data/protamine/PRM1/paml/M0/2NG.dN
examples/evol/data/protamine/PRM1/paml/M0/2NG.dS
examples/evol/data/protamine/PRM1/paml/M0/2NG.t
examples/evol/data/protamine/PRM1/paml/M0/4fold.nuc
examples/evol/data/protamine/PRM1/paml/M0/algn
examples/evol/data/protamine/PRM1/paml/M0/lnf
examples/evol/data/protamine/PRM1/paml/M0/out
examples/evol/data/protamine/PRM1/paml/M0/rst
examples/evol/data/protamine/PRM1/paml/M0/rst1
examples/evol/data/protamine/PRM1/paml/M0/rub
examples/evol/data/protamine/PRM1/paml/M0/tmp.ctl
examples/evol/data/protamine/PRM1/paml/M0/tree
examples/evol/data/protamine/PRM1/paml/M1/2NG.dN
examples/evol/data/protamine/PRM1/paml/M1/2NG.dS
examples/evol/data/protamine/PRM1/paml/M1/2NG.t
examples/evol/data/protamine/PRM1/paml/M1/4fold.nuc
examples/evol/data/protamine/PRM1/paml/M1/M1.out
examples/evol/data/protamine/PRM1/paml/M1/algn
examples/evol/data/protamine/PRM1/paml/M1/lnf
examples/evol/data/protamine/PRM1/paml/M1/rst
examples/evol/data/protamine/PRM1/paml/M1/rst1
examples/evol/data/protamine/PRM1/paml/M1/rub
examples/evol/data/protamine/PRM1/paml/M1/tmp.ctl
examples/evol/data/protamine/PRM1/paml/M1/tree
examples/evol/data/protamine/PRM1/paml/M2/2NG.dN
examples/evol/data/protamine/PRM1/paml/M2/2NG.dS
examples/evol/data/protamine/PRM1/paml/M2/2NG.t
examples/evol/data/protamine/PRM1/paml/M2/4fold.nuc
examples/evol/data/protamine/PRM1/paml/M2/M2.out
examples/evol/data/protamine/PRM1/paml/M2/algn
examples/evol/data/protamine/PRM1/paml/M2/lnf
examples/evol/data/protamine/PRM1/paml/M2/rst
examples/evol/data/protamine/PRM1/paml/M2/rst1
examples/evol/data/protamine/PRM1/paml/M2/rub
examples/evol/data/protamine/PRM1/paml/M2/tmp.ctl
examples/evol/data/protamine/PRM1/paml/M2/tree
examples/evol/data/protamine/PRM1/paml/M7/2NG.dN
examples/evol/data/protamine/PRM1/paml/M7/2NG.dS
examples/evol/data/protamine/PRM1/paml/M7/2NG.t
examples/evol/data/protamine/PRM1/paml/M7/4fold.nuc
examples/evol/data/protamine/PRM1/paml/M7/M7.out
examples/evol/data/protamine/PRM1/paml/M7/algn
examples/evol/data/protamine/PRM1/paml/M7/lnf
examples/evol/data/protamine/PRM1/paml/M7/rst
examples/evol/data/protamine/PRM1/paml/M7/rst1
examples/evol/data/protamine/PRM1/paml/M7/rub
examples/evol/data/protamine/PRM1/paml/M7/tmp.ctl
examples/evol/data/protamine/PRM1/paml/M7/tree
examples/evol/data/protamine/PRM1/paml/M8/2NG.dN
examples/evol/data/protamine/PRM1/paml/M8/2NG.dS
examples/evol/data/protamine/PRM1/paml/M8/2NG.t
examples/evol/data/protamine/PRM1/paml/M8/4fold.nuc
examples/evol/data/protamine/PRM1/paml/M8/M8.out
examples/evol/data/protamine/PRM1/paml/M8/algn
examples/evol/data/protamine/PRM1/paml/M8/lnf
examples/evol/data/protamine/PRM1/paml/M8/rst
examples/evol/data/protamine/PRM1/paml/M8/rst1
examples/evol/data/protamine/PRM1/paml/M8/rub
examples/evol/data/protamine/PRM1/paml/M8/tmp.ctl
examples/evol/data/protamine/PRM1/paml/M8/tree
examples/evol/data/protamine/PRM1/paml/fb/2NG.dN
examples/evol/data/protamine/PRM1/paml/fb/2NG.dS
examples/evol/data/protamine/PRM1/paml/fb/2NG.t
examples/evol/data/protamine/PRM1/paml/fb/4fold.nuc
examples/evol/data/protamine/PRM1/paml/fb/algn
examples/evol/data/protamine/PRM1/paml/fb/fb.out
examples/evol/data/protamine/PRM1/paml/fb/lnf
examples/evol/data/protamine/PRM1/paml/fb/rst.fb
examples/evol/data/protamine/PRM1/paml/fb/rst1
examples/evol/data/protamine/PRM1/paml/fb/rub
examples/evol/data/protamine/PRM1/paml/fb/tmp.ctl
examples/evol/data/protamine/PRM1/paml/fb/tree
examples/evol/data/protamine/PRM1/slr/2NG.dN
examples/evol/data/protamine/PRM1/slr/2NG.dS
examples/evol/data/protamine/PRM1/slr/2NG.t
examples/evol/data/protamine/PRM1/slr/4fold.nuc
examples/evol/data/protamine/PRM1/slr/algn
examples/evol/data/protamine/PRM1/slr/fb.out
examples/evol/data/protamine/PRM1/slr/lnf
examples/evol/data/protamine/PRM1/slr/rst.fb
examples/evol/data/protamine/PRM1/slr/rst1
examples/evol/data/protamine/PRM1/slr/rub
examples/evol/data/protamine/PRM1/slr/slr.ctl
examples/evol/data/protamine/PRM1/slr/tmp.ctl
examples/evol/data/protamine/PRM1/slr/tree
examples/evol/data/protamine/PRM1/slr/tree.slr
examples/general/add_features.py
examples/general/byoperand_search.py
examples/general/chimp.png
examples/general/copy_and_paste_trees.py
examples/general/create_trees_from_scratch.py
examples/general/custom_search.py
examples/general/custom_tree_traversing.py
examples/general/custom_tree_visualization.py
examples/general/dog.png
examples/general/fish.png
examples/general/fly.png
examples/general/genes_tree.nh
examples/general/get_common_ancestor.py
examples/general/get_distances_between_nodes.py
examples/general/get_midpoint_outgroup.py
examples/general/getting_leaves.py
examples/general/human.png
examples/general/iterators.py
examples/general/label_nodes.py
examples/general/mouse.png
examples/general/nhx_format.py
examples/general/prune_tree.py
examples/general/random_tree.png
examples/general/read_newick.py
examples/general/remove_and_delete_nodes.py
examples/general/render_tree_images.py
examples/general/rooting_subtrees.py
examples/general/rooting_trees.py
examples/general/search_nodes.py
examples/general/tree_basis.py
examples/general/tree_traverse.py
examples/general/write_newick.py
examples/nexml/02_dogfish_no_taxrefs.xml
examples/nexml/characters.xml
examples/nexml/meta_taxa.xml
examples/nexml/nexml.xml
examples/nexml/nexml_annotated_trees.py
examples/nexml/nexml_from_scratch.py
examples/nexml/nexml_parser.py
examples/nexml/phenoscape.xml
examples/nexml/taxa.xml
examples/nexml/timetree.xml
examples/nexml/tolweb.xml
examples/nexml/trees.xml
examples/phylogenies/dating_evolutionary_events.py
examples/phylogenies/link_sequences_to_phylogenies.py
examples/phylogenies/orthology_and_paralogy_prediction.py
examples/phylogenies/phylotree.png
examples/phylogenies/phylotree_visualization.py
examples/phylogenies/species_aware_phylogenies.py
examples/phylogenies/tree_reconciliation.py
examples/phyloxml/apaf.xml
examples/phyloxml/bcl_2.xml
examples/phyloxml/example1.xml
examples/phyloxml/example2.xml
examples/phyloxml/example3.xml
examples/phyloxml/multiple_supports.xml
examples/phyloxml/ncbi_taxonomy_metazoa.xml.bz2
examples/phyloxml/phyloxml_examples.xml
examples/phyloxml/phyloxml_from_scratch.py
examples/phyloxml/phyloxml_parser.py
examples/phyloxml/tol_life_on_earth.xml.bz2
examples/treeview/barchart_and_piechart_faces.py
examples/treeview/barcharts.png
examples/treeview/bubble_map.png
examples/treeview/bubble_map.py
examples/treeview/face_grid.py
examples/treeview/face_positions.py
examples/treeview/face_rotation.py
examples/treeview/float_piechart.png
examples/treeview/floating_piecharts.py
examples/treeview/item_faces.png
examples/treeview/item_faces.py
examples/treeview/new_seq_face.py
examples/treeview/node_background.png
examples/treeview/node_background.py
examples/treeview/node_style.png
examples/treeview/node_style.py
examples/treeview/random_draw.py
examples/treeview/rotated_faces.png
examples/treeview/seq_motif_faces.png
examples/treeview/seq_motif_faces.py
examples/treeview/seqmotif.png
examples/treeview/tree_faces.png
examples/treeview/tree_faces.py
examples/treeview/img_faces/chimp.png
examples/treeview/img_faces/dog.png
examples/treeview/img_faces/fish.png
examples/treeview/img_faces/fly.png
examples/treeview/img_faces/human.png
examples/treeview/img_faces/img_faces.png
examples/treeview/img_faces/img_faces.py
examples/treeview/img_faces/mouse.png
examples/webplugin/README
examples/webplugin/close.png
examples/webplugin/ete.css
examples/webplugin/ete.js
examples/webplugin/icon_attachment.png
examples/webplugin/icon_cancel_search.png
examples/webplugin/icon_search.png
examples/webplugin/icon_tools.png
examples/webplugin/jquery-1.4.2.min.js
examples/webplugin/jquery-ui-1.8.4.custom.min.js
examples/webplugin/loader.gif
examples/webplugin/webplugin_example.html
examples/webplugin/wsgi/webplugin_example.py