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 aphylogeo.utils module appendDashToShorterSeqs() (aphylogeo.alignement.AlignSequences method)

B

bootSingle() (in module aphylogeo.utils)

buttler() (aphylogeo.multiProcessor.Multi method)

C

calculateAverageBootstrap() (in module aphylogeo.utils) climaticPipeline() (in module aphylogeo.utils) clustalAlign() (aphylogeo.alignement.AlignSequences method) convert_alignment_to_simple_format() (in module aphylogeo.utils)

createBoostrap() (in module aphylogeo.utils) createClimaticList() (in module aphylogeo.utils) createGeneticList() (in module aphylogeo.utils) createTmpFasta() (in module aphylogeo.utils) createTree() (in module aphylogeo.utils)

D

dictToFile() (aphylogeo.alignement.AlignSequences method)

dictToJson() (in module aphylogeo.utils)

E

euclideanDist() (in module aphylogeo.utils) executeOnce() (aphylogeo.multiProcessor.Multi method)

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

F

fasttree() (in module aphylogeo.utils) fasttreeCMD() (in module aphylogeo.utils) fileToAlignIO() (aphylogeo.alignement.AlignSequences method) fileToDict() (aphylogeo.alignement.AlignSequences method)

filterResults() (in module aphylogeo.utils) format_to_csv() (in module aphylogeo.utils) from_dict() (aphylogeo.alignement.Alignment class method) from_fasta_file() (aphylogeo.alignement.Alignment class method) from_json_string() (aphylogeo.alignement.Alignment class method)

G

geneticPipeline() (in module aphylogeo.utils) 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) getData() (in module aphylogeo.utils) getDissimilaritiesMatrix() (in module aphylogeo.utils) getSequenceCentroid() (aphylogeo.alignement.AlignSequences method)

H

header() (in module aphylogeo.utils)

I

insertDash() (aphylogeo.alignement.AlignSequences method)

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

L

leastSquare() (in module aphylogeo.utils) load_climatic_trees() (in module aphylogeo.utils) 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) loadSequenceFile() (in module aphylogeo.utils)

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 aphylogeo.utils

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)

R

reverse_climatic_pipeline() (in module aphylogeo.utils)

robinsonFoulds() (in module aphylogeo.utils)

S

save_climatic_trees() (in module aphylogeo.utils) 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)

W

writeOutputFile() (in module aphylogeo.utils)