Index

A

annotateNwk_nextstrain() (in module scripts.defineAndCountClades) annotateNwk_treetime() (in module scripts.defineAndCountClades) assignCladeToLin() (in module scripts.defineAndCountClades)

assignToNucMut() (in module scripts.defineAndCountClades) assignToSpecAA() (in module scripts.defineAndCountClades) assignToTraits() (in module scripts.defineAndCountClades)

C

Clade (class in scripts.drawMuller)

CladeSnapshot (class in scripts.drawMuller) countAbudanceFromNames_byWeek() (in module scripts.defineAndCountClades)

D

defineChildBoundries() (in module scripts.drawMuller)

drawWrapper() (in module scripts.drawMuller)

E

extractCord_draw() (in module scripts.drawMuller)

M

main() (in module scripts.defineAndCountClades) (in module scripts.drawMuller) (in module scripts.mutationLinages_report) (in module scripts.parseFastaNames) makeColor() (in module scripts.drawMuller)

module scripts.defineAndCountClades scripts.drawMuller scripts.mutationLinages_report scripts.parseFastaNames

R

readInMeta() (in module scripts.defineAndCountClades)

removeSmallClades() (in module scripts.drawMuller)

S

scripts.defineAndCountClades module scripts.drawMuller module scripts.mutationLinages_report module

scripts.parseFastaNames module Snapshot (class in scripts.drawMuller) sumUpDescendants() (scripts.drawMuller.CladeSnapshot method)

T

textheight() (in module scripts.drawMuller) textwidth() (in module scripts.drawMuller)

timeToX() (in module scripts.drawMuller) treetimeToTraits_d() (in module scripts.defineAndCountClades)