Index

A

adaptive decrement

addon options

B

bicodon adaptation index

bicodon usage

C

codon adaptation index (CAI) options codon usage conda

configuration conservative start related to start codon structure custom scoring function

D

degradation

DegScore options

F

fitness quick start tuning

folding options full scan

G

GC content

genetic algorithm

H

hairpin

I

iCodon options troubleshooting with pip in-cell stability

in-solution stability inverted repeat iteration quick start tuning

L

leader sequence LinearDesign guide initialization installation options removing tandem repeat tuning example tutorial VaxPress as a front-end interface

long stem loop

M

metric minimum free energy (MFE) multi-core

multi-thread mutation rate options tuning

O

offspring optimization guide options

options output

P

parallelization options persistent settings pip plugin

population tuning preset guide options

R

random seed repeat report options report only

rpy2

S

score scoring function quick start short tandem repeat

singularity start codon options stem length survivor

T

tandem repeat

total loop length

U

uridine options

W

weight

winddown rate winddown trigger