Index

A

add() (treemaker.Tree method) (treemaker.TreeMaker method) (treemaker.treemaker.Tree method) (treemaker.treemaker.TreeMaker method)

add_from() (treemaker.TreeMaker method) (treemaker.treemaker.TreeMaker method)

G

get() (treemaker.Tree method) (treemaker.treemaker.Tree method)

get_or_create() (treemaker.Tree method) (treemaker.treemaker.Tree method)

I

is_node (treemaker.Tree attribute) (treemaker.treemaker.Tree attribute)

is_tip (treemaker.Tree attribute) (treemaker.treemaker.Tree attribute)

M

main() (in module treemaker.treemaker)

P

parse_args() (in module treemaker.treemaker)

parse_classification() (treemaker.TreeMaker method) (treemaker.treemaker.TreeMaker method)

R

read() (treemaker.TreeMaker method) (treemaker.treemaker.TreeMaker method)

S

setUpClass() (treemaker.test_treemaker.Test_TreeMakerIO class method)

T

tearDownClass() (treemaker.test_treemaker.Test_TreeMakerIO class method) test_add() (treemaker.test_treemaker.Test_Tree method) (treemaker.test_treemaker.Test_TreeMaker method) test_add_2() (treemaker.test_treemaker.Test_TreeMaker method) test_add_from() (treemaker.test_treemaker.Test_TreeMaker method) test_add_from_exception() (treemaker.test_treemaker.Test_TreeMaker method) test_conflicts() (treemaker.test_treemaker.Test_Tree method) test_deep_tree() (treemaker.test_treemaker.Test_Tree method) (treemaker.test_treemaker.Test_Tree_Nodelabels method) test_empty_tree() (treemaker.test_treemaker.Test_Tree method) test_eq() (treemaker.test_treemaker.Test_Tree method) test_error_on_bad_taxon() (treemaker.test_treemaker.Test_TreeMaker method) test_error_on_duplicate() (treemaker.test_treemaker.Test_TreeMaker method) test_example() (treemaker.test_treemaker.Test_Tree method) (treemaker.test_treemaker.Test_Tree_Nodelabels method) test_get() (treemaker.test_treemaker.Test_Tree method) test_get_or_create() (treemaker.test_treemaker.Test_Tree method) test_gt() (treemaker.test_treemaker.Test_Tree method) test_IOError_on_no_file() (treemaker.test_treemaker.Test_ParseArgs method) test_is_node() (treemaker.test_treemaker.Test_Tree method) test_is_tip() (treemaker.test_treemaker.Test_Tree method) test_lt() (treemaker.test_treemaker.Test_Tree method) test_parse_classification() (treemaker.test_treemaker.Test_TreeMaker method) test_parse_filename_and_full_output() (treemaker.test_treemaker.Test_ParseArgs method) test_parse_filename_and_output() (treemaker.test_treemaker.Test_ParseArgs method) test_parse_filename_only() (treemaker.test_treemaker.Test_ParseArgs method) test_parse_mode() (treemaker.test_treemaker.Test_ParseArgs method) test_parse_nodelabels() (treemaker.test_treemaker.Test_ParseArgs method) Test_ParseArgs (class in treemaker.test_treemaker) test_read() (treemaker.test_treemaker.Test_TreeMakerIO method) test_read_error_on_malformed() (treemaker.test_treemaker.Test_TreeMakerIO method)

test_read_skips_empty_lines() (treemaker.test_treemaker.Test_TreeMakerIO method) test_read_with_tabs() (treemaker.test_treemaker.Test_TreeMakerIO method) test_real() (treemaker.test_treemaker.Test_Tree method) (treemaker.test_treemaker.Test_Tree_Nodelabels method) test_recursive_add() (treemaker.test_treemaker.Test_Tree method) (treemaker.test_treemaker.Test_Tree_Nodelabels method) test_repr() (treemaker.test_treemaker.Test_Tree method) test_sanitise() (treemaker.test_treemaker.Test_Tree method) test_simple() (treemaker.test_treemaker.Test_Tree method) (treemaker.test_treemaker.Test_Tree_Nodelabels method) test_singleton_tree() (treemaker.test_treemaker.Test_Tree method) test_tips() (treemaker.test_treemaker.Test_Tree method) Test_Tree (class in treemaker.test_treemaker) Test_Tree_Nodelabels (class in treemaker.test_treemaker) Test_TreeMaker (class in treemaker.test_treemaker) Test_TreeMakerIO (class in treemaker.test_treemaker) test_write_newick() (treemaker.test_treemaker.Test_TreeMakerIO method) test_write_nexus() (treemaker.test_treemaker.Test_TreeMakerIO method) test_write_nexus_error_on_bad_method() (treemaker.test_treemaker.Test_TreeMakerIO method) test_write_to_file_error_on_existing_file() (treemaker.test_treemaker.Test_TreeMakerIO method) test_write_to_file_error_on_invalid_mode() (treemaker.test_treemaker.Test_TreeMakerIO method) test_write_to_newick() (treemaker.test_treemaker.Test_TreeMakerIO method) test_write_to_nexus() (treemaker.test_treemaker.Test_TreeMakerIO method) tips() (treemaker.Tree method) (treemaker.treemaker.Tree method) Tree (class in treemaker) (class in treemaker.treemaker) TreeMaker (class in treemaker) (class in treemaker.treemaker) treemaker (module) treemaker.test_treemaker (module) treemaker.treemaker (module)

W

write() (treemaker.TreeMaker method) (treemaker.treemaker.TreeMaker method)

write_to_file() (treemaker.TreeMaker method) (treemaker.treemaker.TreeMaker method)