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W
_
__init__() (wgd.codeml.Codeml method)
(wgd.utils.Genome method)
(wgd.utils.gaussian_kde method)
_calculate_weighted_ks() (in module wgd.ks_distribution)
_calculate_weights() (in module wgd.ks_distribution)
_compute_covariance() (wgd.utils.gaussian_kde method)
_get_nucleotide_sequences() (in module wgd.ks_distribution)
_random_color() (in module wgd.utils)
_weighting() (in module wgd.ks_distribution)
_write_gene_lists() (in module wgd.colinearity)
A
add_alignment_stats() (in module wgd.ks_distribution)
align() (in module wgd.alignment)
align_mafft() (in module wgd.alignment)
align_muscle() (in module wgd.alignment)
align_prank() (in module wgd.alignment)
all_v_all_blast() (in module wgd.blast_mcl)
analyse_family() (in module wgd.ks_distribution)
analyse_family_pairwise() (in module wgd.ks_distribution)
ava_blast_to_abc() (in module wgd.blast_mcl)
average_linkage_clustering() (in module wgd.phy)
B
blast_mcl() (in module wgd_cli)
C
can_i_run_software() (in module wgd.utils)
check_dirs() (in module wgd.utils)
Codeml (class in wgd.codeml)
E
evaluate() (wgd.utils.gaussian_kde method)
F
filter_group_data() (in module wgd.modeling)
filter_one_vs_one_families() (in module wgd.utils)
fit_bgmm() (in module wgd.modeling)
fit_gmm() (in module wgd.modeling)
G
gaussian_kde (class in wgd.utils)
Genome (class in wgd.utils)
get_anchor_pairs() (in module wgd.colinearity)
get_array_for_mixture() (in module wgd.modeling)
get_component_probabilities() (in module wgd.modeling)
get_gfs_for_species() (in module wgd.utils)
get_one_v_one_orthologs_rbh() (in module wgd.blast_mcl)
get_pairwise_alns() (in module wgd.alignment)
get_paralogs_fasta() (in module wgd.utils)
get_sequences() (in module wgd.utils)
H
hamming_distance() (in module wgd.alignment)
histogram_bokeh() (in module wgd.viz)
I
inspect_aic() (in module wgd.modeling)
inspect_bic() (in module wgd.modeling)
K
karyotype_json() (wgd.utils.Genome method)
kde_() (in module wgd_cli)
ks_analysis_one_vs_one() (in module wgd.ks_distribution)
ks_analysis_paranome() (in module wgd.ks_distribution)
ksd_() (in module wgd_cli)
L
log_subprocess() (in module wgd.utils)
M
mix_() (in module wgd_cli)
P
pairwise_alignment_stats() (in module wgd.alignment)
pal2nal() (in module wgd.alignment)
parse_plaza_gff() (wgd.utils.Genome method)
phylogenetic_tree_to_cluster_format() (in module wgd.phy)
plot_aic_bic() (in module wgd.modeling)
plot_all_models_bgmm() (in module wgd.modeling)
plot_all_models_gmm() (in module wgd.modeling)
plot_bars_weights() (in module wgd.modeling)
plot_dists() (in module wgd.viz)
plot_mixture() (in module wgd.modeling)
plot_probs() (in module wgd.modeling)
plot_selection() (in module wgd.viz)
prepare_aln() (in module wgd.alignment)
process_gene_families() (in module wgd.utils)
R
read_fasta() (in module wgd.utils)
reflect() (in module wgd.modeling)
reflected_kde() (in module wgd.modeling)
run_adhore() (in module wgd.colinearity)
run_codeml() (wgd.codeml.Codeml method)
run_fasttree() (in module wgd.phy)
run_mcl_ava() (in module wgd.blast_mcl)
run_phyml() (in module wgd.phy)
S
segments_to_chords_table() (in module wgd.colinearity)
set_bandwidth() (wgd.utils.gaussian_kde method)
sort_families_by_size() (in module wgd.ks_distribution)
strip_gaps_pair() (in module wgd.alignment)
syn_() (in module wgd_cli)
syntenic_dotplot() (in module wgd.viz)
syntenic_dotplot_ks_colored() (in module wgd.viz)
T
translate_cds() (in module wgd.utils)
U
uniq_id() (in module wgd.utils)
V
viz_() (in module wgd_cli)
W
wgd.alignment (module)
wgd.blast_mcl (module)
wgd.codeml (module)
wgd.colinearity (module)
wgd.ks_distribution (module)
wgd.modeling (module)
wgd.phy (module)
wgd.utils (module)
wgd.viz (module)
wgd_cli (module)
write_alignment_codeml() (in module wgd.alignment)
write_config_adhore() (in module wgd.colinearity)
write_families_file() (in module wgd.colinearity)
write_fasta() (in module wgd.utils)
write_sequential_phyml() (in module wgd.phy)
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