SCORPiOs
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Input Data Preparation
Data preparation
Data file formats
Configuration file
Building a dataset
Outputs Description
Corrected gene trees
Tree visualization
Intermediary outputs
LORelEi (LORe Extension)
Introducing SCORPiOs LORelEi
LORelEi usage instructions
LORelEi configuration file
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SCORPiOs
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Index
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C
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D
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I
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M
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N
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W
A
add_gene() (in module scripts.synteny.utilities)
(scripts.synteny.mygenome.Genome method)
add_legend() (in module scripts.lorelei.fix_rideogram)
add_nhx_tags() (in module scripts.trees.genetree)
add_nhx_tags_and_rm_sp() (in module scripts.trees.regraft_subtrees)
all_duplicate_genes (scripts.synteny.utilities.GeneFamily attribute)
all_reduce_in_two_blocks() (scripts.synteny.syntenycompare.DupSegments method)
are_species_sep() (in module scripts.graphs.orthogroups)
B
barplot() (in module scripts.lorelei.homeologs_tree_conflicts)
beginning() (scripts.synteny.mygenome.Gene property)
branch_length_closest() (in module scripts.trees.genetree)
C
check_aore_consistent_tree() (in module scripts.lorelei.constrained_aore_lore_topologies)
check_copy_number() (in module scripts.lorelei.constrained_aore_lore_topologies)
check_orthology() (in module scripts.synteny.syntenycompare)
choose_best_graph() (in module scripts.graphs.combine_outgroups)
chr_list (scripts.synteny.mygenome.Genome attribute)
Chromosome (scripts.synteny.mygenome.ContigType attribute)
chromosome() (scripts.synteny.mygenome.Gene property)
(scripts.synteny.mygenome.GenePosition property)
chromosomes (scripts.synteny.syntenycompare.DupSegments attribute)
closest_gene_in_tree() (in module scripts.trees.genetree)
collapse_nodes() (in module scripts.graphs.orthogroups)
color_internal_node() (in module scripts.trees.make_tree_images)
color_leaves() (in module scripts.trees.make_tree_images)
combine_outgroups() (in module scripts.graphs.combine_outgroups)
complete_load_orthotable() (in module scripts.synteny.utilities)
compute_f1() (in module scripts.synteny.f1_score_optimization)
contig_type() (in module scripts.synteny.mygenome)
ContigType (class in scripts.synteny.mygenome)
contracted_nodes() (in module scripts.graphs.orthogroups)
convert_ali() (in module scripts.trees.convert_ids)
convert_tree() (in module scripts.trees.convert_ids)
copy_nhx_tags() (in module scripts.trees.genetree)
corr_tag_below_node() (in module scripts.trees.iteration_nhx_tags)
correct_wtrees() (in module scripts.trees.regraft_subtrees)
count() (in module scripts.trees.parse_au_test)
D
delete_gaps_in_all() (in module scripts.trees.utilities)
dict_genes (scripts.synteny.mygenome.Genome attribute)
DupSegments (class in scripts.synteny.syntenycompare)
E
end() (scripts.synteny.mygenome.Gene property)
extract_subtrees() (in module scripts.lorelei.constrained_aore_lore_topologies)
F
family_ids (scripts.synteny.syntenycompare.DupSegments attribute)
FamilyOrthologies (class in scripts.trees.inconsistent_trees)
features_to_ide() (in module scripts.lorelei.make_rideograms_inputs)
find_best_threading() (in module scripts.synteny.pairwise_orthology_synteny)
find_closest() (in module scripts.synteny.utilities)
find_node_with_most_desc() (in module scripts.trees.genetree)
find_sister_of_outgroup() (in module scripts.trees.genetree)
find_synteny_orthologs() (in module scripts.synteny.missed_orthologies)
G
Gene (class in scripts.synteny.mygenome)
GeneFamily (class in scripts.synteny.utilities)
GenePosition (class in scripts.synteny.mygenome)
genes_dict (scripts.synteny.syntenycompare.DupSegments attribute)
genes_list (scripts.synteny.mygenome.Genome attribute)
GeneSpeciesPosition (in module scripts.synteny.utilities)
Genome (class in scripts.synteny.mygenome)
get_all_chromosome_and_position() (in module scripts.synteny.utilities)
get_all_chromosomes_involved() (in module scripts.synteny.utilities)
get_all_outgr_names() (in module scripts.synteny.utilities)
get_all_outgr_pos() (in module scripts.synteny.utilities)
get_anc_order() (in module scripts.trees.speciestree)
get_corrected_wgd_nodes() (in module scripts.trees.make_tree_images)
get_discriminant_threshold() (in module scripts.synteny.f1_score_optimization)
get_genes_positions() (in module scripts.synteny.duplicated_families)
get_genes_to_keep() (in module scripts.synteny.filter_regions)
get_inconsistent_trees() (in module scripts.trees.inconsistent_trees)
get_modified_families() (in module scripts.synteny.filter_regions)
get_orthogroups_genes() (in module scripts.trees.cut_subtrees)
get_score() (scripts.synteny.syntenycompare.DupSegments method)
get_scorpios_aore_tree() (in module scripts.lorelei.constrained_aore_lore_topologies)
get_sister_species() (in module scripts.trees.speciestree)
get_solution_subtree() (in module scripts.trees.genetree)
get_speciation_events() (in module scripts.trees.orthologs)
get_species() (in module scripts.trees.speciestree)
get_species_groups() (in module scripts.lorelei.constrained_aore_lore_topologies)
get_subali() (in module scripts.trees.utilities)
H
hypergeom_enrich_depl() (in module scripts.lorelei.homeologs_tree_conflicts)
I
identify_outgroup_vs_wgd_subtree() (in module scripts.trees.make_tree_images)
index() (scripts.synteny.mygenome.GenePosition property)
init_other_attributes() (scripts.synteny.mygenome.Genome method)
init_worker() (in module scripts.graphs.orthogroups)
(in module scripts.trees.build_treebest_trees)
(in module scripts.trees.regraft_subtrees)
insert_outgr_gene() (in module scripts.synteny.utilities)
involved_chromosomes (scripts.synteny.utilities.GeneFamily attribute)
is_below() (in module scripts.trees.speciestree)
is_bz2() (in module scripts.synteny.mygenome)
is_multigenic() (scripts.trees.inconsistent_trees.FamilyOrthologies method)
is_speciation() (in module scripts.trees.orthologs)
K
keep_sis_genes_together() (in module scripts.trees.genetree)
keep_subsequent_wgd_species() (in module scripts.trees.genetree)
L
lazy_load_pairwise_file() (in module scripts.graphs.orthogroups)
light_load_orthotable() (in module scripts.synteny.utilities)
load_acc() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
load_combin() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
load_corrections() (in module scripts.trees.genetree)
load_counts() (in module scripts.lorelei.homeologs_tree_conflicts)
load_features() (in module scripts.lorelei.make_rideograms_inputs)
load_gene_list() (in module scripts.lorelei.write_ancgenes_treeclass)
load_genes() (in module scripts.synteny.missed_orthologies)
load_line() (in module scripts.graphs.orthogroups)
load_orthotable() (in module scripts.synteny.utilities)
load_outgr_fam() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
load_pm() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
load_pred_file() (in module scripts.trees.inconsistent_trees)
load_scores() (in module scripts.synteny.f1_score_optimization)
load_summary() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
load_tree_orthologies() (in module scripts.synteny.pairwise_orthology_synteny)
lore_aore_summary() (in module scripts.trees.parse_au_test)
M
make_all_figures() (in module scripts.trees.make_tree_images)
make_karyo() (in module scripts.lorelei.make_rideograms_inputs)
make_legend() (in module scripts.lorelei.fix_rideogram)
make_region_file() (in module scripts.synteny.filter_regions)
make_tree_figure() (in module scripts.trees.make_tree_images)
make_tree_from_groups() (in module scripts.lorelei.constrained_aore_lore_topologies)
map_families_across_outgr() (in module scripts.graphs.combine_outgroups)
matrix (scripts.synteny.syntenycompare.DupSegments attribute)
merge_trees_and_write() (in module scripts.trees.merge_subtrees)
min_cut() (in module scripts.graphs.orthogroups)
Mitochondrial (scripts.synteny.mygenome.ContigType attribute)
module
scripts.graphs.combine_outgroups
scripts.graphs.orthogroups
scripts.lorelei.constrained_aore_lore_topologies
scripts.lorelei.fix_rideogram
scripts.lorelei.homeologs_pairs_from_ancestor
scripts.lorelei.homeologs_tree_conflicts
scripts.lorelei.make_rideograms_inputs
scripts.lorelei.write_ancgenes_treeclass
scripts.synteny.duplicated_families
scripts.synteny.f1_score_optimization
scripts.synteny.filter_no_synteny_genes
scripts.synteny.filter_regions
scripts.synteny.missed_orthologies
scripts.synteny.mygenome
scripts.synteny.pairwise_orthology_synteny
scripts.synteny.syntenycompare
scripts.synteny.utilities
scripts.trees.build_treebest_trees
scripts.trees.convert_ids
scripts.trees.cut_subtrees
scripts.trees.genetree
scripts.trees.inconsistent_trees
scripts.trees.iteration_nhx_tags
scripts.trees.make_tree_images
scripts.trees.merge_subtrees
scripts.trees.orthologs
scripts.trees.parse_au_test
scripts.trees.regraft_subtrees
scripts.trees.speciestree
scripts.trees.utilities
most_central_edge() (in module scripts.graphs.orthogroups)
multiprocess_rec_brlgth() (in module scripts.trees.regraft_subtrees)
N
name (scripts.synteny.mygenome.Genome attribute)
names() (scripts.synteny.mygenome.Gene property)
neighbour_outgr_ortholog() (in module scripts.synteny.missed_orthologies)
O
one_file_consel() (in module scripts.trees.parse_au_test)
one_file_consel_3_trees() (in module scripts.trees.parse_au_test)
orthologies_with_outgroup() (in module scripts.synteny.duplicated_families)
orthologs_score() (scripts.synteny.syntenycompare.DupSegments method)
outgr_chr (scripts.synteny.utilities.GeneFamily attribute)
outgr_chromosomes() (in module scripts.synteny.utilities)
outgr_genename (scripts.synteny.utilities.GeneFamily attribute)
outgr_position (scripts.synteny.utilities.GeneFamily attribute)
outgroup_genes_to_homeologs() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
P
plot_sign() (in module scripts.lorelei.homeologs_tree_conflicts)
print_out_stats() (in module scripts.graphs.orthogroups)
(in module scripts.synteny.duplicated_families)
(in module scripts.synteny.filter_no_synteny_genes)
(in module scripts.synteny.filter_regions)
(in module scripts.synteny.missed_orthologies)
(in module scripts.trees.inconsistent_trees)
R
Random (scripts.synteny.mygenome.ContigType attribute)
read_authorized_regions() (in module scripts.synteny.filter_regions)
read_combin_file() (in module scripts.synteny.filter_regions)
read_multiple_objects() (in module scripts.trees.utilities)
read_summary() (in module scripts.graphs.combine_outgroups)
remove_anc() (in module scripts.trees.speciestree)
remove_outgroup() (in module scripts.trees.merge_subtrees)
retention_loss_score() (scripts.synteny.syntenycompare.DupSegments method)
S
save_nhx_tags() (in module scripts.trees.genetree)
Scaffold (scripts.synteny.mygenome.ContigType attribute)
scripts.graphs.combine_outgroups
module
scripts.graphs.orthogroups
module
scripts.lorelei.constrained_aore_lore_topologies
module
scripts.lorelei.fix_rideogram
module
scripts.lorelei.homeologs_pairs_from_ancestor
module
scripts.lorelei.homeologs_tree_conflicts
module
scripts.lorelei.make_rideograms_inputs
module
scripts.lorelei.write_ancgenes_treeclass
module
scripts.synteny.duplicated_families
module
scripts.synteny.f1_score_optimization
module
scripts.synteny.filter_no_synteny_genes
module
scripts.synteny.filter_regions
module
scripts.synteny.missed_orthologies
module
scripts.synteny.mygenome
module
scripts.synteny.pairwise_orthology_synteny
module
scripts.synteny.syntenycompare
module
scripts.synteny.utilities
module
scripts.trees.build_treebest_trees
module
scripts.trees.convert_ids
module
scripts.trees.cut_subtrees
module
scripts.trees.genetree
module
scripts.trees.inconsistent_trees
module
scripts.trees.iteration_nhx_tags
module
scripts.trees.make_tree_images
module
scripts.trees.merge_subtrees
module
scripts.trees.orthologs
module
scripts.trees.parse_au_test
module
scripts.trees.regraft_subtrees
module
scripts.trees.speciestree
module
scripts.trees.utilities
module
search_closest_neighbours() (in module scripts.synteny.missed_orthologies)
search_one_node() (in module scripts.trees.speciestree)
sort() (scripts.synteny.syntenycompare.DupSegments method)
species_name() (in module scripts.graphs.orthogroups)
split_chr_with_ohnologs() (in module scripts.synteny.utilities)
strip_chr_name() (in module scripts.lorelei.make_rideograms_inputs)
synteny_orthology_prediction() (in module scripts.synteny.pairwise_orthology_synteny)
T
tag_duplicated_species() (in module scripts.synteny.duplicated_families)
to_constrained_tree() (scripts.trees.inconsistent_trees.FamilyOrthologies method)
to_dup_segments() (in module scripts.synteny.syntenycompare)
toint() (in module scripts.synteny.mygenome)
topo_changes() (in module scripts.trees.regraft_subtrees)
U
update_constrained_tree() (scripts.trees.inconsistent_trees.FamilyOrthologies method)
update_discard() (scripts.synteny.syntenycompare.DupSegments method)
update_orthologies() (scripts.synteny.syntenycompare.DupSegments method)
(scripts.trees.inconsistent_trees.FamilyOrthologies method)
update_orthologytable() (in module scripts.synteny.utilities)
W
worker_build_tree() (in module scripts.trees.build_treebest_trees)
worker_cut_graph() (in module scripts.graphs.orthogroups)
worker_rec_brlgth() (in module scripts.trees.regraft_subtrees)
write_ancgenes() (in module scripts.lorelei.write_ancgenes_treeclass)
write_counter() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
write_fasta() (in module scripts.trees.utilities)
write_forest() (in module scripts.trees.utilities)
write_orthologies() (in module scripts.synteny.pairwise_orthology_synteny)
write_orthologs() (in module scripts.synteny.duplicated_families)
write_output() (in module scripts.lorelei.homeologs_pairs_from_ancestor)
write_regions_file() (in module scripts.synteny.filter_regions)
write_resolved_tree() (in module scripts.trees.cut_subtrees)
write_summary() (in module scripts.lorelei.write_ancgenes_treeclass)
write_updated_orthotable() (in module scripts.synteny.utilities)
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