Index

A

assembly() (in module pyphylogenomics.NGS)

B

batch_iterator() (in module pyphylogenomics.BLAST) batchAlignment() (in module pyphylogenomics.MUSCLE) blastn() (in module pyphylogenomics.BLAST)

blastParser() (in module pyphylogenomics.BLAST) bluntSplicer() (in module pyphylogenomics.MUSCLE)

C

count_reads() (in module pyphylogenomics.NGS)

D

designPrimers() (in module pyphylogenomics.MUSCLE)

do_blast() (in module pyphylogenomics.BLAST)

E

eraseFalsePosi() (in module pyphylogenomics.BLAST)

F

filter_reads() (in module pyphylogenomics.NGS) filterByMinDist() (in module pyphylogenomics.BLAST)

find_index_in_seq() (in module pyphylogenomics.NGS)

G

get_cds() (in module pyphylogenomics.BLAST) get_velvet_params() (in module pyphylogenomics.NGS)

getLargestExon() (in module pyphylogenomics.BLAST) guess_best_kmer() (in module pyphylogenomics.NGS)

L

levenshtein() (in module pyphylogenomics.NGS)

M

makeblastdb() (in module pyphylogenomics.BLAST)

O

OrthoDB (class in pyphylogenomics._orthodb)

P

parse_blast_results() (in module pyphylogenomics.NGS) place_seq_in_frame() (in module pyphylogenomics.BLAST) prepare_data() (in module pyphylogenomics.NGS) prune() (in module pyphylogenomics.NGS) pyphylogenomics.__init__ (module)

pyphylogenomics._orthodb (module) pyphylogenomics.BLAST (module) pyphylogenomics.MUSCLE (module) pyphylogenomics.NGS (module)

Q

quality_control() (in module pyphylogenomics.NGS)

S

separate_by_index() (in module pyphylogenomics.NGS) split_ionfile_by_results() (in module pyphylogenomics.NGS)

split_results_file() (in module pyphylogenomics.NGS) storeExonsInFrame() (in module pyphylogenomics.BLAST)

T

trim_seq() (in module pyphylogenomics.BLAST)

W

wellSeparatedExons() (in module pyphylogenomics.BLAST)