[cogent3.app]
align_to_ref=cogent3.app.align:align_to_ref
ancestral_states=cogent3.app.evo:ancestral_states
approx_jc69=cogent3.app.dist:approx_jc69
approx_pdist=cogent3.app.dist:approx_pdist
bootstrap=cogent3.app.evo:bootstrap
cogent3_score=cogent3.app.align:cogent3_score
concat=cogent3.app.sample:concat
fast_slow_dist=cogent3.app.dist:fast_slow_dist
fixed_length=cogent3.app.sample:fixed_length
gap_dist=cogent3.app.dist:gap_dist
hypothesis=cogent3.app.evo:hypothesis
ic_score=cogent3.app.align:ic_score
jaccard_dist=cogent3.app.dist:jaccard_dist
load_aligned=cogent3.app.io:load_aligned
load_db=cogent3.app.io:load_db
load_json=cogent3.app.io:load_json
load_tabular=cogent3.app.io:load_tabular
load_unaligned=cogent3.app.io:load_unaligned
min_length=cogent3.app.sample:min_length
model=cogent3.app.evo:model
model_collection=cogent3.app.evo:model_collection
natsel_neutral=cogent3.app.evo:natsel_neutral
natsel_sitehet=cogent3.app.evo:natsel_sitehet
natsel_timehet=cogent3.app.evo:natsel_timehet
natsel_zhang=cogent3.app.evo:natsel_zhang
omit_bad_seqs=cogent3.app.sample:omit_bad_seqs
omit_degenerates=cogent3.app.sample:omit_degenerates
omit_duplicated=cogent3.app.sample:omit_duplicated
omit_gap_pos=cogent3.app.sample:omit_gap_pos
progressive_align=cogent3.app.align:progressive_align
quick_tree=cogent3.app.tree:quick_tree
scale_branches=cogent3.app.tree:scale_branches
select_translatable=cogent3.app.translate:select_translatable
smith_waterman=cogent3.app.align:smith_waterman
sp_score=cogent3.app.align:sp_score
tabulate_stats=cogent3.app.evo:tabulate_stats
take_codon_positions=cogent3.app.sample:take_codon_positions
take_n_seqs=cogent3.app.sample:take_n_seqs
take_named_seqs=cogent3.app.sample:take_named_seqs
translate_seqs=cogent3.app.translate:translate_seqs
trim_stop_codons=cogent3.app.sample:trim_stop_codons
uniformize_tree=cogent3.app.tree:uniformize_tree
write_db=cogent3.app.io:write_db
write_json=cogent3.app.io:write_json
write_seqs=cogent3.app.io:write_seqs
write_tabular=cogent3.app.io:write_tabular

[cogent3.format.sequence]
fasta=cogent3.format.sequence:FastaWriter
gde=cogent3.format.sequence:GdeWriter
paml=cogent3.format.sequence:PamlWriter
phylip=cogent3.format.sequence:PhylipWriter

[cogent3.load.annotations]
c3andb=cogent3.core.annotation_db:SqliteAnnotationDbLoader
c3anndb=cogent3.core.annotation_db:SqliteAnnotationDbLoader
c3gbdb=cogent3.core.annotation_db:SqliteAnnotationDbLoader
c3gffdb=cogent3.core.annotation_db:SqliteAnnotationDbLoader

[cogent3.parse.sequence]
clustal=cogent3.parse.sequence:ClustalParser
fasta=cogent3.parse.sequence:FastaParser
gbseq=cogent3.parse.sequence:GbSeqParser
gde=cogent3.parse.sequence:GdeParser
genbank=cogent3.parse.sequence:GenbankParser
msf=cogent3.parse.sequence:MsfParser
nexus=cogent3.parse.sequence:NexusParser
paml=cogent3.parse.sequence:PamlParser
phylip=cogent3.parse.sequence:PhylipParser
tinyseq=cogent3.parse.sequence:TinyseqParser

