Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

aabgcolors (in ete2.treeview.faces)	aitemfreq() (in ete2.clustering.stats)	asETE() (in ete2.coretype.tree)
aabut() (in ete2.clustering.pstat)	akendalltau() (in ete2.clustering.stats)	ashellsort() (in ete2.clustering.stats)
aafgcolors (in ete2.treeview.faces)	akruskalwallish() (in ete2.clustering.stats)	asign() (in ete2.clustering.stats)
abetacf() (in ete2.clustering.stats)	aks_2samp() (in ete2.clustering.stats)	asignaltonoise() (in ete2.clustering.stats)
abetai() (in ete2.clustering.stats)	aksprob() (in ete2.clustering.stats)	askew() (in ete2.clustering.stats)
abut() (in ete2.clustering.pstat)	akurtosis() (in ete2.clustering.stats)	askewtest() (in ete2.clustering.stats)
achisqprob() (in ete2.clustering.stats)	akurtosistest() (in ete2.clustering.stats)	asortrows() (in ete2.clustering.pstat)
achisquare() (in ete2.clustering.stats)	alincc() (in ete2.clustering.stats)	aspearmanr() (in ete2.clustering.stats)
acolex() (in ete2.clustering.pstat)	alinexand() (in ete2.clustering.pstat)	asquare_of_sums() (in ete2.clustering.stats)
acollapse() (in ete2.clustering.pstat)	alinexor() (in ete2.clustering.pstat)	asRphylo() (in ete2.coretype.tree)
acorrelation() (in ete2.clustering.stats)	alinregress() (in ete2.clustering.stats)	ass() (in ete2.clustering.stats)
acov() (in ete2.clustering.stats)	amannwhitneyu() (in ete2.clustering.stats)	astdev() (in ete2.clustering.stats)
acovariance() (in ete2.clustering.stats)	amasslinregress() (in ete2.clustering.stats)	asterr() (in ete2.clustering.stats)
acumfreq() (in ete2.clustering.stats)	amean() (in ete2.clustering.stats)	asum() (in ete2.clustering.stats)
acumsum() (in ete2.clustering.stats)	amedian() (in ete2.clustering.stats)	asumdiffsquared() (in ete2.clustering.stats)
add_branch() (in _TreeScene)	amedianscore() (in ete2.clustering.stats)	asummult() (in ete2.clustering.stats)
add_child() (in TreeNode)	amode() (in ete2.clustering.stats)	athreshold() (in ete2.clustering.stats)
add_childs() (in _NodeItem)	amoment() (in ete2.clustering.stats)	atiecorrect() (in ete2.clustering.stats)
add_face_to_node() (in ete2.treeview.faces)	anormaltest() (in ete2.clustering.stats)	atmax() (in ete2.clustering.stats)
add_faces() (in _TreeScene)	aobrientransform() (in ete2.clustering.stats)	atmean() (in ete2.clustering.stats)
add_feature() (in TreeNode)	ap2t() (in ete2.clustering.stats)	atmin() (in ete2.clustering.stats)
add_feature() (in NewickDialog)	apaired() (in ete2.clustering.stats)	atrim1() (in ete2.clustering.stats)
add_features() (in TreeNode)	apearsonr() (in ete2.clustering.stats)	atrimboth() (in ete2.clustering.stats)
add_scale() (in _TreeScene)	apercentileofscore() (in ete2.clustering.stats)	atsem() (in ete2.clustering.stats)
add_sister() (in TreeNode)	apointbiserialr() (in ete2.clustering.stats)	atstdev() (in ete2.clustering.stats)
adescribe() (in ete2.clustering.stats)	apply_changes() (in _PropertiesDialog)	attest_1samp() (in ete2.clustering.stats)
adm() (in ete2.clustering.pstat)	arankdata() (in ete2.clustering.stats)	attest_ind() (in ete2.clustering.stats)
aduplicates() (in ete2.clustering.pstat)	aranksums() (in ete2.clustering.stats)	attest_rel() (in ete2.clustering.stats)
aerfcc() (in ete2.clustering.stats)	arecode() (in ete2.clustering.pstat)	AttrFace (in ete2.treeview.faces)
aF_oneway() (in ete2.clustering.stats)	arelfreq() (in ete2.clustering.stats)	atvar() (in ete2.clustering.stats)
aF_value() (in ete2.clustering.stats)	areplace() (in ete2.clustering.pstat)	aunique() (in ete2.clustering.pstat)
afindwithin() (in ete2.clustering.stats)	arowcompare() (in ete2.clustering.pstat)	avar() (in ete2.clustering.stats)
afprob() (in ete2.clustering.stats)	arowsame() (in ete2.clustering.pstat)	avariation() (in ete2.clustering.stats)
afriedmanchisquare() (in ete2.clustering.stats)	arraytable (in ete2.coretype)	awilcoxont() (in ete2.clustering.stats)
agammln() (in ete2.clustering.stats)	ArrayTable (in ete2.coretype.arraytable)	az() (in ete2.clustering.stats)
ageometricmean() (in ete2.clustering.stats)	asamplestdev() (in ete2.clustering.stats)	azmap() (in ete2.clustering.stats)
aglm() (in ete2.clustering.stats)	asamplevar() (in ete2.clustering.stats)	azprob() (in ete2.clustering.stats)
aharmonicmean() (in ete2.clustering.stats)	ascoreatpercentile() (in ete2.clustering.stats)	azs() (in ete2.clustering.stats)
ahistogram() (in ete2.clustering.stats)	asem() (in ete2.clustering.stats)

B

back_to_parent_node() (in _NodeItem)	betacf (in ete2.clustering.stats)
basic() (in ete2.treeview.layouts)	betai (in ete2.clustering.stats)

C

CacheMode	cluster_lines() (in ete2.treeview.layouts)	commitAndCloseEditor() (in _TableItem)
CacheMode	clustering (in ete2)	coretype (in ete2)
CacheModeFlag	ClusterNode (in ete2.clustering.clustertree)	count_algs() (in PhylomeDBConnector)
children (in TreeNode)	clustertree (in ete2.clustering)	count_trees() (in PhylomeDBConnector)
chisqprob (in ete2.clustering.stats)	clustvalidation (in ete2.clustering)	createEditor() (in _TableItem)
chisquare (in ete2.clustering.stats)	colex() (in ete2.clustering.pstat)	cumfreq (in ete2.clustering.stats)
cluster_bars() (in ete2.treeview.layouts)	collapse() (in ete2.clustering.pstat)	cumsum (in ete2.clustering.stats)
cluster_cbars() (in ete2.treeview.layouts)	collapse() (in TreeNode)	cut_partition() (in _NodeItem)

D

DEBUG (in ete2.treeview.drawer)	describe() (in TreeNode)	DockOptions
DEFAULT_COMPACT (in ete2.coretype.tree)	detach() (in TreeNode)	DragMode
DEFAULT_DIST (in ete2.parser.newick)	detach_node() (in _NodeItem)	draw() (in _TreeScene)
DEFAULT_NAME (in ete2.parser.newick)	deviation (in ClusterNode)	draw_bar_profile() (in ProfileFace)
DEFAULT_SHOWINTERNAL (in ete2.coretype.tree)	DialogCode	draw_centered_bar_profile() (in ProfileFace)
DEFAULT_SUPPORT (in ete2.parser.newick)	dices() (in ete2.clustering.stats)	draw_heatmap_profile() (in ProfileFace)
del_feature() (in TreeNode)	Dispatch (in ete2.clustering.stats)	draw_line_profile() (in ProfileFace)
del_feature() (in NewickDialog)	displayText() (in _TableItem)	drawer (in ete2.treeview)
delete() (in TreeNode)	dist (in TreeNode)	duplicates() (in ete2.clustering.pstat)
delete_node() (in _NodeItem)	dm() (in ete2.clustering.pstat)
describe (in ete2.clustering.stats)	DockOption

E

EndEditHint	ete_resources_rc (in ete2.treeview)	evolevents (in ete2.phylo)
erfcc (in ete2.clustering.stats)	euclidean_dist() (in ete2.clustering.clustvalidation)	expand() (in TreeNode)
ete2	EvolEvent (in ete2.phylo.evolevents)

F

F_oneway (in ete2.clustering.stats)	faces (in ete2.treeview)	flat() (in ete2.clustering.pstat)
F_value (in ete2.clustering.stats)	fasta (in ete2.parser)	format_node() (in ete2.parser.newick)
F_value_multivariate() (in ete2.clustering.stats)	findwithin (in ete2.clustering.stats)	fprob (in ete2.clustering.stats)
Face (in ete2.treeview.faces)	fit_to_scale() (in ProfileFace)	friedmanchisquare (in ete2.clustering.stats)

G

gammln (in ete2.clustering.stats)	get_farthest_leaf() (in TreeNode)	get_raw_alg() (in PhylomeDBConnector)
geometricmean (in ete2.clustering.stats)	get_farthest_node() (in TreeNode)	get_reconciled_tree() (in ete2.phylo.reconciliation)
get_age() (in PhyloNode)	get_farthest_oldest_leaf() (in PhyloNode)	get_row_vector() (in ArrayTable)
get_algs() (in PhylomeDBConnector)	get_id_by_external() (in PhylomeDBConnector)	get_seed_ids() (in PhylomeDBConnector)
get_ascii() (in TreeNode)	get_id_translations() (in PhylomeDBConnector)	get_selected_nodes() (in _SelectorItem)
get_available_trees() (in PhylomeDBConnector)	get_leaf_names() (in TreeNode)	get_seq() (in SeqGroup)
get_available_trees_by_phylome() (in PhylomeDBConnector)	get_leaf_profiles() (in ClusterNode)	get_seqid_info() (in PhylomeDBConnector)
get_available_trees_in_phylome() (in PhylomeDBConnector)	get_leaves() (in TreeNode)	get_seqids_in_proteome() (in PhylomeDBConnector)
get_average_centroid_linkage_dist() (in ete2.coretype.arraytable)	get_leaves_by_name() (in TreeNode)	get_seqs_in_proteome() (in PhylomeDBConnector)
get_avg_profile() (in ete2.clustering.clustvalidation)	get_longest_isoform() (in PhylomeDBConnector)	get_several_column_vectors() (in ArrayTable)
get_best_tree() (in PhylomeDBConnector)	get_max_vector() (in ete2.coretype.arraytable)	get_several_row_vectors() (in ArrayTable)
get_centroid_dist() (in ete2.coretype.arraytable)	get_mean_vector() (in ete2.coretype.arraytable)	get_silhouette() (in ClusterNode)
get_children() (in TreeNode)	get_median_vector() (in ete2.coretype.arraytable)	get_silhouette_width() (in ete2.clustering.clustvalidation)
get_clean_alg() (in PhylomeDBConnector)	get_midpoint_outgroup() (in TreeNode)	get_sisters() (in TreeNode)
get_collateral_seeds() (in PhylomeDBConnector)	get_min_vector() (in ete2.coretype.arraytable)	get_species() (in PhyloNode)
get_color_gradient() (in ProfileFace)	get_my_evol_events() (in PhyloNode)	get_species() (in PhylomeDBConnector)
get_column_vector() (in ArrayTable)	get_orthologs() (in PhylomeDBConnector)	get_species_info() (in PhylomeDBConnector)
get_common_ancestor() (in TreeNode)	get_phylome_algs() (in PhylomeDBConnector)	get_text() (in AttrFace)
get_descendant_evol_events() (in PhyloNode)	get_phylome_info() (in PhylomeDBConnector)	get_text() (in TextFace)
get_descendants() (in TreeNode)	get_phylome_trees() (in PhylomeDBConnector)	get_tree() (in PhylomeDBConnector)
get_distance() (in TreeNode)	get_phylomes() (in PhylomeDBConnector)	get_tree_root() (in TreeNode)
get_dunn() (in ClusterNode)	get_prop_table() (in _PropertiesDialog)	GraphicsItemChange
get_dunn_index() (in ete2.clustering.clustvalidation)	get_props_in_nodes() (in _PropertiesDialog)	GraphicsItemFlag
get_entries() (in SeqGroup)	get_proteome_info() (in PhylomeDBConnector)	GraphicsItemFlags
get_evol_events_from_leaf() (in ete2.phylo.spoverlap)	get_proteomes() (in PhylomeDBConnector)
get_evol_events_from_root() (in ete2.phylo.spoverlap)	get_proteomes_in_phylome() (in PhylomeDBConnector)

H

harmonicmean (in ete2.clustering.stats)	hoverEnterEvent() (in _FaceItem)	hoverLeaveEvent() (in _NodeItem)
heatmap() (in ete2.treeview.layouts)	hoverEnterEvent() (in _NodeItem)	hoverLeaveEvent() (in _TextItem)
highlight_node() (in _TreeScene)	hoverEnterEvent() (in _TextItem)
histogram (in ete2.clustering.stats)	hoverLeaveEvent() (in _FaceItem)

I

icc() (in ete2.clustering.stats)	is_monophyletic() (in PhyloNode)	iter_descendants() (in TreeNode)
ImgFace (in ete2.treeview.faces)	is_root() (in TreeNode)	iter_entries() (in SeqGroup)
incr (in ete2.clustering.stats)	isActive() (in _SelectorItem)	iter_leaf_names() (in TreeNode)
initialize_tree_scene() (in _TreeScene)	isstring() (in ete2.clustering.pstat)	iter_leaf_profiles() (in ClusterNode)
intercluster_dist (in ClusterNode)	isSupportedType() (in _TableItem)	iter_leaves() (in TreeNode)
intracluster_dist (in ClusterNode)	itemfreq (in ete2.clustering.stats)	iter_search_nodes() (in TreeNode)
is_leaf() (in TreeNode)	ItemIndexMethod	iter_species() (in PhyloNode)

K

kendalltau (in ete2.clustering.stats)	ks_2samp (in ete2.clustering.stats)	kurtosistest (in ete2.clustering.stats)
keyPressEvent() (in _MainView)	ksprob (in ete2.clustering.stats)
kruskalwallish (in ete2.clustering.stats)	kurtosis (in ete2.clustering.stats)

L

large() (in ete2.treeview.layouts)	link_to_alignment() (in PhyloNode)	lsamplestdev() (in ete2.clustering.stats)
layout_functions (in ete2.treeview.layouts)	link_to_arraytable() (in ClusterNode)	lsamplevar() (in ete2.clustering.stats)
layouts (in ete2.treeview)	linregress (in ete2.clustering.stats)	lscoreatpercentile() (in ete2.clustering.stats)
lbetacf() (in ete2.clustering.stats)	list2string() (in ete2.clustering.pstat)	lsem() (in ete2.clustering.stats)
lbetai() (in ete2.clustering.stats)	litemfreq() (in ete2.clustering.stats)	lshellsort() (in ete2.clustering.stats)
lchisqprob() (in ete2.clustering.stats)	lkendalltau() (in ete2.clustering.stats)	lskew() (in ete2.clustering.stats)
lchisquare() (in ete2.clustering.stats)	lkruskalwallish() (in ete2.clustering.stats)	lspearmanr() (in ete2.clustering.stats)
lcov() (in ete2.clustering.stats)	lks_2samp() (in ete2.clustering.stats)	lsquare_of_sums() (in ete2.clustering.stats)
lcumfreq() (in ete2.clustering.stats)	lksprob() (in ete2.clustering.stats)	lss() (in ete2.clustering.stats)
lcumsum() (in ete2.clustering.stats)	lkurtosis() (in ete2.clustering.stats)	lstdev() (in ete2.clustering.stats)
ldescribe() (in ete2.clustering.stats)	llincc() (in ete2.clustering.stats)	lsterr() (in ete2.clustering.stats)
lerfcc() (in ete2.clustering.stats)	llinregress() (in ete2.clustering.stats)	lsum() (in ete2.clustering.stats)
lF_oneway() (in ete2.clustering.stats)	lmannwhitneyu() (in ete2.clustering.stats)	lsumdiffsquared() (in ete2.clustering.stats)
lF_value() (in ete2.clustering.stats)	lmean() (in ete2.clustering.stats)	lsummult() (in ete2.clustering.stats)
lfindwithin() (in ete2.clustering.stats)	lmedian() (in ete2.clustering.stats)	ltiecorrect() (in ete2.clustering.stats)
lfprob() (in ete2.clustering.stats)	lmedianscore() (in ete2.clustering.stats)	ltrim1() (in ete2.clustering.stats)
lfriedmanchisquare() (in ete2.clustering.stats)	lmode() (in ete2.clustering.stats)	ltrimboth() (in ete2.clustering.stats)
lgammln() (in ete2.clustering.stats)	lmoment() (in ete2.clustering.stats)	lttest_1samp() (in ete2.clustering.stats)
lgeometricmean() (in ete2.clustering.stats)	load_pixmap_from_file() (in Face)	lttest_ind() (in ete2.clustering.stats)
lharmonicmean() (in ete2.clustering.stats)	lobrientransform() (in ete2.clustering.stats)	lttest_rel() (in ete2.clustering.stats)
lhistogram() (in ete2.clustering.stats)	logger() (in ete2.treeview.drawer)	lvar() (in ete2.clustering.stats)
lincc (in ete2.clustering.stats)	lpaired() (in ete2.clustering.stats)	lvariation() (in ete2.clustering.stats)
lincr() (in ete2.clustering.stats)	lpearsonr() (in ete2.clustering.stats)	lwilcoxont() (in ete2.clustering.stats)
linedelimited() (in ete2.clustering.pstat)	lpercentileofscore() (in ete2.clustering.stats)	lz() (in ete2.clustering.stats)
lineincols() (in ete2.clustering.pstat)	lpointbiserialr() (in ete2.clustering.stats)	lzprob() (in ete2.clustering.stats)
lineincustcols() (in ete2.clustering.pstat)	lrankdata() (in ete2.clustering.stats)	lzs() (in ete2.clustering.stats)
linexand() (in ete2.clustering.pstat)	lranksums() (in ete2.clustering.stats)
linexor() (in ete2.clustering.pstat)	lrelfreq() (in ete2.clustering.stats)

M

makelol() (in ete2.clustering.pstat)	mode (in ete2.clustering.stats)	mousePressEvent() (in _TreeScene)
makestr() (in ete2.clustering.pstat)	moment (in ete2.clustering.stats)	mouseReleaseEvent() (in _FaceItem)
mannwhitneyu (in ete2.clustering.stats)	mouseDoubleClickEvent() (in _TreeScene)	mouseReleaseEvent() (in _NodeItem)
mean (in ete2.clustering.stats)	mouseMoveEvent() (in _TreeScene)	mouseReleaseEvent() (in _TextItem)
median (in ete2.clustering.stats)	mousePressEvent() (in _FaceItem)	mouseReleaseEvent() (in _TreeScene)
medianscore (in ete2.clustering.stats)	mousePressEvent() (in _NodeItem)
merge_columns() (in ArrayTable)	mousePressEvent() (in _TextItem)

N

O

obrientransform (in ete2.clustering.stats)	on_actionPaste_newick_triggered() (in _MainApp)	on_actionZoomInX_triggered() (in _MainApp)
on_actionBranchLength_triggered() (in _MainApp)	on_actionRender_selected_region_triggered() (in _MainApp)	on_actionZoomInY_triggered() (in _MainApp)
on_actionChange_orientation_triggered() (in _MainApp)	on_actionRenderPDF_triggered() (in _MainApp)	on_actionZoomOut_triggered() (in _MainApp)
on_actionClear_search_triggered() (in _MainApp)	on_actionSave_newick_triggered() (in _MainApp)	on_actionZoomOutX_triggered() (in _MainApp)
on_actionETE_triggered() (in _MainApp)	on_actionSearchNode_triggered() (in _MainApp)	on_actionZoomOutY_triggered() (in _MainApp)
on_actionFit2region_triggered() (in _MainApp)	on_actionShow_newick_triggered() (in _MainApp)	OptimizationFlag
on_actionFit2tree_triggered() (in _MainApp)	on_actionShow_phenogram_triggered() (in _MainApp)	OptimizationFlags
on_actionForceTopology_triggered() (in _MainApp)	on_actionShowCladogram_triggered() (in _MainApp)	outputfstats() (in ete2.clustering.stats)
on_actionOpen_triggered() (in _MainApp)	on_actionZoomIn_triggered() (in _MainApp)	outputpairedstats() (in ete2.clustering.stats)

P

paint() (in _HighlighterItem)	phylip (in ete2.parser)	populate_partition() (in _NodeItem)
paint() (in _NodeItem)	phylo (in ete2)	print_supported_formats() (in ete2.parser.newick)
paint() (in _SelectorItem)	phylogeny() (in ete2.treeview.layouts)	printcc() (in ete2.clustering.pstat)
paint() (in _TableItem)	phylomedb (in ete2)	printincols() (in ete2.clustering.pstat)
PaintDeviceMetric	phylomeDB (in ete2.phylomedb)	printl() (in ete2.clustering.pstat)
paired (in ete2.clustering.stats)	PhylomeDBConnector (in ete2.phylomedb.phylomeDB)	profile (in ClusterNode)
parser (in ete2)	PhyloNode (in ete2.phylo.phylotree)	ProfileFace (in ete2.treeview.faces)
paste_partition() (in _NodeItem)	phylotree (in ete2.phylo)	prune() (in TreeNode)
pearson_dist() (in ete2.clustering.clustvalidation)	pl() (in ete2.clustering.pstat)	pstat (in ete2.clustering)
pearsonr (in ete2.clustering.stats)	pointbiserialr (in ete2.clustering.stats)
percentileofscore (in ete2.clustering.stats)	populate() (in TreeNode)

Q

qCleanupResources() (in ete2.treeview.ete_resources_rc)	qt_resource_data (in ete2.treeview.ete_resources_rc)	qt_resource_struct (in ete2.treeview.ete_resources_rc)
qInitResources() (in ete2.treeview.ete_resources_rc)	qt_resource_name (in ete2.treeview.ete_resources_rc)

R

rankdata (in ete2.clustering.stats)	remap() (in ete2.clustering.pstat)	resizeEvent() (in _MainView)
ranksums (in ete2.clustering.stats)	remove_child() (in TreeNode)	retranslateUi() (in Ui_About)
read_arraytable() (in ete2.parser.text_arraytable)	remove_column() (in ArrayTable)	retranslateUi() (in Ui_MainWindow)
read_fasta() (in ete2.parser.fasta)	remove_sister() (in TreeNode)	retranslateUi() (in Ui_OpenNewick)
read_newick() (in ete2.parser.newick)	render() (in TreeNode)	retranslateUi() (in Ui_Dialog)
read_phylip() (in ete2.parser.phylip)	render_node() (in _TreeScene)	retranslateUi() (in Ui_Newick)
recode() (in ete2.clustering.pstat)	render_tree() (in ete2.treeview.drawer)	ROOTED_PHYLOMES (in ete2)
reconcile() (in PhyloNode)	RenderFlag	ROOTED_PHYLOMES (in ete2.phylomedb.phylomeDB)
reconciliation (in ete2.phylo)	RenderFlags	rotate_node() (in _TreeScene)
relfreq (in ete2.clustering.stats)	replace() (in ete2.clustering.pstat)	roundlist() (in ete2.clustering.pstat)

S

safe_mean() (in ete2.clustering.clustvalidation)	set_seq() (in SeqGroup)	skew (in ete2.clustering.stats)
safe_mean() (in ete2.coretype.arraytable)	set_species_naming_function() (in PhyloNode)	skewtest (in ete2.clustering.stats)
safe_mean_vector() (in ete2.clustering.clustvalidation)	set_start_node() (in _NodeItem)	sortby() (in ete2.clustering.pstat)
safe_mean_vector() (in ete2.coretype.arraytable)	set_style_from() (in _TreeScene)	spearman_dist() (in ete2.clustering.clustvalidation)
safe_scale() (in _MainView)	setActive() (in _SelectorItem)	spearmanr (in ete2.clustering.stats)
samplestdev (in ete2.clustering.stats)	setEditorData() (in _TableItem)	species (in PhyloNode)
samplevar (in ete2.clustering.stats)	setupUi() (in Ui_About)	species_ages (in ete2.phylomedb)
save() (in _TreeScene)	setupUi() (in Ui_MainWindow)	spoverlap (in ete2.phylo)
save_by_chunks() (in _TreeScene)	setupUi() (in Ui_OpenNewick)	square_euclidean_dist() (in ete2.clustering.clustvalidation)
SceneLayer	setupUi() (in Ui_Dialog)	square_of_sums (in ete2.clustering.stats)
SceneLayers	setupUi() (in Ui_Newick)	ss (in ete2.clustering.stats)
scoreatpercentile (in ete2.clustering.stats)	Shadow	stats (in ete2.clustering)
search_id() (in PhylomeDBConnector)	Shape	stdev (in ete2.clustering.stats)
search_nodes() (in TreeNode)	ShapeMode	sterr (in ete2.clustering.stats)
sem (in ete2.clustering.stats)	shellsort (in ete2.clustering.stats)	StyleMask
seqgroup (in ete2.coretype)	show() (in TreeNode)	sum (in ete2.clustering.stats)
SeqGroup (in ete2.coretype.seqgroup)	show_newick() (in _NodeItem)	sumdiffsquared (in ete2.clustering.stats)
SequenceFace (in ete2.treeview.faces)	show_tree() (in ete2.treeview.drawer)	summult (in ete2.clustering.stats)
set_as_outgroup() (in _NodeItem)	showActionPopup() (in _NodeItem)	support (in TreeNode)
set_custom_features() (in NewickDialog)	signaltonoise (in ete2.clustering.stats)	swap_branches() (in _NodeItem)
set_distance_function() (in ClusterNode)	silhouette (in ClusterNode)	swap_childs() (in TreeNode)
set_outgroup() (in TreeNode)	simpleabut() (in ete2.clustering.pstat)

T

text_arraytable (in ete2.parser)	traverse() (in TreeNode)	trimboth (in ete2.clustering.stats)
TextFace (in ete2.treeview.faces)	tree (in ete2.coretype)	tsem (in ete2.clustering.stats)
threshold (in ete2.clustering.stats)	TreeError (in ete2.coretype.tree)	tstdev (in ete2.clustering.stats)
tiecorrect (in ete2.clustering.stats)	TreeImageProperties (in ete2.treeview.drawer)	ttest_1samp (in ete2.clustering.stats)
tmean (in ete2.clustering.stats)	TreeNode (in ete2.coretype.tree)	ttest_ind (in ete2.clustering.stats)
toggle_collapse() (in _NodeItem)	treeview (in ete2)	ttest_rel (in ete2.clustering.stats)
transpose() (in ArrayTable)	trim1 (in ete2.clustering.stats)	tvar (in ete2.clustering.stats)

U

Ui_About (in ete2.treeview._about)	unique() (in ete2.clustering.pstat)	update_pixmap() (in ImgFace)
Ui_Dialog (in ete2.treeview._search_dialog)	unroot() (in TreeNode)	update_pixmap() (in ProfileFace)
Ui_MainWindow (in ete2.treeview._mainwindow)	up (in TreeNode)	update_pixmap() (in SequenceFace)
Ui_Newick (in ete2.treeview._show_newick)	update_newick() (in NewickDialog)	update_pixmap() (in ValidationFace)
Ui_OpenNewick (in ete2.treeview._open_newick)	update_node_areas() (in _TreeScene)	update_properties() (in _PropertiesDialog)
unhighlight_node() (in _TreeScene)	update_pixmap() (in Face)	USE_GL (in ete2.treeview.drawer)

V

ValidationFace (in ete2.treeview.faces)	variation (in ete2.clustering.stats)	ViewportUpdateMode
var (in ete2.clustering.stats)	ViewportAnchor	void() (in _NodeItem)

W

wheelEvent() (in _MainView)	write() (in TreeNode)	write_phylip() (in ete2.parser.phylip)
wilcoxont (in ete2.clustering.stats)	write_arraytable() (in ete2.parser.text_arraytable)	writecc() (in ete2.clustering.stats)
write() (in ArrayTable)	write_fasta() (in ete2.parser.fasta)
write() (in SeqGroup)	write_newick() (in ete2.parser.newick)

Z

z (in ete2.clustering.stats)	zprob (in ete2.clustering.stats)	zs (in ete2.clustering.stats)

_

__add__() (in TreeNode)	__package__ (in ete2.phylo.reconciliation)	_get_children() (in TreeNode)
__and__() (in TreeNode)	__package__ (in ete2.phylo.spoverlap)	_get_dist() (in TreeNode)
__call__() (in Dispatch)	__package__ (in ete2.phylomedb)	_get_expected_topology() (in ete2.phylo.reconciliation)
__contains__() (in SeqGroup)	__package__ (in ete2.phylomedb.phylomeDB)	_get_features_string() (in ete2.parser.newick)
__contains__() (in TreeNode)	__package__ (in ete2.treeview)	_get_inter() (in ClusterNode)
__init__() (in ClusterNode)	__package__ (in ete2.treeview._about)	_get_intra() (in ClusterNode)
__init__() (in Dispatch)	__package__ (in ete2.treeview._mainwindow)	_get_prof() (in ClusterNode)
__init__() (in ArrayTable)	__package__ (in ete2.treeview._open_newick)	_get_silh() (in ClusterNode)
__init__() (in SeqGroup)	__package__ (in ete2.treeview._search_dialog)	_get_species() (in PhyloNode)
__init__() (in TreeError)	__package__ (in ete2.treeview._show_newick)	_get_species_on_TOL() (in ete2.phylo.reconciliation)
__init__() (in TreeNode)	__package__ (in ete2.treeview.drawer)	_get_std() (in ClusterNode)
__init__() (in EvolEvent)	__package__ (in ete2.treeview.ete_resources_rc)	_get_support() (in TreeNode)
__init__() (in PhyloNode)	__package__ (in ete2.treeview.faces)	_get_up() (in TreeNode)
__init__() (in PhylomeDBConnector)	__package__ (in ete2.treeview.layouts)	_height() (in Face)
__init__() (in NewickDialog)	__str__() (in ArrayTable)	_height() (in TextFace)
__init__() (in TreeImageProperties)	__str__() (in SeqGroup)	_HighlighterItem (in ete2.treeview.drawer)
__init__() (in _FaceItem)	__str__() (in TreeError)	_humanv1 (in ete2.phylomedb)
__init__() (in _HighlighterItem)	__str__() (in TreeNode)	_ILEGAL_NEWICK_CHARS (in ete2.parser.newick)
__init__() (in _MainApp)	__VERSION__ (in ete2)	_iter_descendants_postorder() (in TreeNode)
__init__() (in _MainView)	__VERSION__ (in ete2.clustering)	_iter_descendants_preorder() (in TreeNode)
__init__() (in _NodeItem)	__VERSION__ (in ete2.clustering.clustertree)	_link_names2matrix() (in ArrayTable)
__init__() (in _PropModeChooser)	__VERSION__ (in ete2.clustering.clustvalidation)	_MainApp (in ete2.treeview.drawer)
__init__() (in _PropertiesDialog)	__VERSION__ (in ete2.clustering.pstat)	_MainView (in ete2.treeview.drawer)
__init__() (in _SelectorItem)	__VERSION__ (in ete2.clustering.stats)	_mainwindow (in ete2.treeview)
__init__() (in _TableItem)	__VERSION__ (in ete2.coretype)	_MIN_NODE_STYLE (in ete2.treeview.drawer)
__init__() (in _TextItem)	__VERSION__ (in ete2.coretype.arraytable)	_NAME_RE (in ete2.parser.newick)
__init__() (in _TreeScene)	__VERSION__ (in ete2.coretype.seqgroup)	_NHX_RE (in ete2.parser.newick)
__init__() (in AttrFace)	__VERSION__ (in ete2.coretype.tree)	_NodeItem (in ete2.treeview.drawer)
__init__() (in Face)	__VERSION__ (in ete2.parser)	_open_newick (in ete2.treeview)
__init__() (in ImgFace)	__VERSION__ (in ete2.parser.fasta)	_parse_extra_features() (in ete2.parser.newick)
__init__() (in ProfileFace)	__VERSION__ (in ete2.parser.newick)	_parse_species() (in ete2.phylo.phylotree)
__init__() (in SequenceFace)	__VERSION__ (in ete2.parser.phylip)	_PropertiesDialog (in ete2.treeview.drawer)
__init__() (in TextFace)	__VERSION__ (in ete2.parser.text_arraytable)	_PropModeChooser (in ete2.treeview.drawer)
__init__() (in ValidationFace)	__VERSION__ (in ete2.phylo)	_QApp (in ete2.treeview.drawer)
__iter__() (in SeqGroup)	__VERSION__ (in ete2.phylo.evolevents)	_read_newick_from_string() (in ete2.parser.newick)
__iter__() (in TreeNode)	__VERSION__ (in ete2.phylo.phylotree)	_read_node_data() (in ete2.parser.newick)
__len__() (in SeqGroup)	__VERSION__ (in ete2.phylo.reconciliation)	_replace_on_template() (in ete2.phylo.reconciliation)
__len__() (in TreeNode)	__VERSION__ (in ete2.phylo.spoverlap)	_search_dialog (in ete2.treeview)
__package__ (in ete2)	__VERSION__ (in ete2.phylomedb)	_SelectorItem (in ete2.treeview.drawer)
__package__ (in ete2.clustering)	__VERSION__ (in ete2.phylomedb.phylomeDB)	_seq2str() (in ete2.parser.fasta)
__package__ (in ete2.clustering.clustertree)	__VERSION__ (in ete2.treeview)	_set_children() (in TreeNode)
__package__ (in ete2.clustering.clustvalidation)	__VERSION__ (in ete2.treeview._about)	_set_dist() (in TreeNode)
__package__ (in ete2.clustering.pstat)	__VERSION__ (in ete2.treeview._mainwindow)	_set_forbidden() (in ClusterNode)
__package__ (in ete2.clustering.stats)	__VERSION__ (in ete2.treeview._open_newick)	_set_profile() (in ClusterNode)
__package__ (in ete2.coretype)	__VERSION__ (in ete2.treeview._search_dialog)	_set_species() (in PhyloNode)
__package__ (in ete2.coretype.arraytable)	__VERSION__ (in ete2.treeview._show_newick)	_set_support() (in TreeNode)
__package__ (in ete2.coretype.seqgroup)	__VERSION__ (in ete2.treeview.drawer)	_set_up() (in TreeNode)
__package__ (in ete2.coretype.tree)	__VERSION__ (in ete2.treeview.ete_resources_rc)	_show_newick (in ete2.treeview)
__package__ (in ete2.parser)	__VERSION__ (in ete2.treeview.faces)	_size() (in Face)
__package__ (in ete2.parser.fasta)	__VERSION__ (in ete2.treeview.layouts)	_TableItem (in ete2.treeview.drawer)
__package__ (in ete2.parser.newick)	_about (in ete2.treeview)	_TextItem (in ete2.treeview.drawer)
__package__ (in ete2.parser.phylip)	_asciiArt() (in TreeNode)	_translate_nodes() (in ete2.coretype.tree)
__package__ (in ete2.parser.text_arraytable)	_calculate_avg_profile() (in ClusterNode)	_TreeScene (in ete2.treeview.drawer)
__package__ (in ete2.phylo)	_execute_block() (in PhylomeDBConnector)	_width() (in AttrFace)
__package__ (in ete2.phylo.evolevents)	_FaceItem (in ete2.treeview.drawer)	_width() (in Face)
__package__ (in ete2.phylo.phylotree)	_FLOAT_RE (in ete2.parser.newick)	_width() (in TextFace)