Index

A

align() (aphylogeo.alignement.AlignSequences method) Alignment (class in aphylogeo.alignement) AlignSequences (class in aphylogeo.alignement) alignSequencesWithPairwise() (aphylogeo.alignement.AlignSequences method) alignSingle() (aphylogeo.alignement.AlignSequences method) aphylogeo.alignement module

aphylogeo.genetic_trees module aphylogeo.multiProcessor module aphylogeo.params module appendDashToShorterSeqs() (aphylogeo.alignement.AlignSequences method)

B

buttler() (aphylogeo.multiProcessor.Multi method)

C

clustalAlign() (aphylogeo.alignement.AlignSequences method)

D

dictToFile() (aphylogeo.alignement.AlignSequences method)

E

executeOnce() (aphylogeo.multiProcessor.Multi method)

executeSmall() (aphylogeo.multiProcessor.Multi method) extractOneAlignAcc() (aphylogeo.alignement.AlignSequences method)

F

fileToAlignIO() (aphylogeo.alignement.AlignSequences method) fileToDict() (aphylogeo.alignement.AlignSequences method)

from_dict() (aphylogeo.alignement.Alignment class method) from_fasta_file() (aphylogeo.alignement.Alignment class method) from_json_string() (aphylogeo.alignement.Alignment class method)

G

GeneticTrees (class in aphylogeo.genetic_trees) get_trees_str() (aphylogeo.genetic_trees.GeneticTrees method) getAlignCouple() (aphylogeo.alignement.AlignSequences method)

getAlignSeqLens() (aphylogeo.alignement.AlignSequences method) getAlignSeqs() (aphylogeo.alignement.AlignSequences method) getSequenceCentroid() (aphylogeo.alignement.AlignSequences method)

I

insertDash() (aphylogeo.alignement.AlignSequences method)

insertDashToShorterSeq() (aphylogeo.alignement.AlignSequences method) isCurrentCharDash() (aphylogeo.alignement.AlignSequences method)

L

load_default_param() (aphylogeo.params.Params class method) load_from_json() (aphylogeo.alignement.Alignment class method)

load_trees_from_file() (aphylogeo.genetic_trees.GeneticTrees class method) load_trees_from_json() (aphylogeo.genetic_trees.GeneticTrees class method)

M

mafftAlign() (aphylogeo.alignement.AlignSequences method) makeMSA() (aphylogeo.alignement.AlignSequences method) memUpdate() (aphylogeo.multiProcessor.Multi method) merge() (aphylogeo.alignement.AlignSequences method) mergeFitPairwise() (aphylogeo.alignement.AlignSequences method) module aphylogeo.alignement aphylogeo.genetic_trees aphylogeo.multiProcessor aphylogeo.params

msa_from_string() (aphylogeo.alignement.Alignment static method) msa_to_string() (aphylogeo.alignement.Alignment static method) Multi (class in aphylogeo.multiProcessor) muscleAlign() (aphylogeo.alignement.AlignSequences method)

N

narrowFitPairwise() (aphylogeo.alignement.AlignSequences method)

P

PARAMETER_KEYS (aphylogeo.params.Params attribute) Params (class in aphylogeo.params)

processingLargeData() (aphylogeo.multiProcessor.Multi method) processingSmallData() (aphylogeo.multiProcessor.Multi method)

S

save_to_json() (aphylogeo.alignement.Alignment method) save_trees_to_json() (aphylogeo.genetic_trees.GeneticTrees method) ScoreSingle() (aphylogeo.alignement.AlignSequences method)

similarity() (aphylogeo.alignement.AlignSequences method) slidingWindow() (aphylogeo.alignement.AlignSequences method) starAlignement() (aphylogeo.alignement.AlignSequences method)

T

terminalUpdate() (aphylogeo.multiProcessor.Multi method)

testtrees() (aphylogeo.genetic_trees.GeneticTrees class method) to_dict() (aphylogeo.alignement.Alignment method)

U

update_from_dict() (aphylogeo.params.Params class method)

V

validate_and_set_params() (aphylogeo.params.Params class method)