-x NUM

Sets the number of iterations after burn-in (default is 50000)

-y NUM

Sets the number of burn-in iterations (default is 50000)

-z NUM

Sets the number of iterations between samples (default is 100)

-e NUM

Sets the number of branch-swapping moves per iterations (default is so that half of the time is spent branch-swapping)

-m NUM

Sets the initial value of theta to NUM (default is Watterson estimate)

-d NUM

Sets the initial value of delta to NUM (default is 0.001)

-n NUM

Sets the initial value of nu to NUM (default is 0.01)

-r NUM

Sets the initial value of R to NUM (default is initial theta/10)

-M

Do update the value of theta

-D

Do not update the value of delta

-N

Do not update the value of nu

-R

Do not update the value of R

-T

Do not update the topology

-A

Do not update the ages of the nodes

-G

Remove all gaps

-H

Remove all gaps at non-polymorphic positions

-t NUM

Indicate which initial tree to use: 0 for a null tree, 1 for a uniformly chosen coalescent tree and 2 for UPGMA tree (default)

-a NUM

Sets the first parameter of the beta prior distribution of nu

-b NUM

Sets the second parameter of the beta prior distribution of nu

-U

Use uniform priors for rho, theta and delta

-B

Run in BURST mode

-C

Run in UPGMA mode with a site-by-site bootstrap procedure

-c

Run in UPGMA mode with a fragment-by-fragment bootstrap procedure

-S NUM

Sets the seed for the random number generator to NUM

-E NUM

Sets the rate of exponential growth (default is 0)

-I

Ignores first block in the alignment

-L

Clean-up the alignment before running ClonalFrame

-l

Minimum distance between two reference sites (default is 50)

-v

Verbose mode