[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

