GLAM2(1) | glam2 Manual | GLAM2(1) |

Show all options and their default
settings.

Output file (*stdout*).

Number of alignment runs (*10*).

End each run after this many iterations
without improvement ( *10000*).

Examine both strands - forward and reverse
complement.

Minimum number of sequences in the alignment
(*2*).

Minimum number of aligned columns
(*2*).

Maximum number of aligned columns
(*50*).

Initial number of aligned columns
(*20*).

Dirichlet mixture file.

Deletion pseudocount (*0.1*).

No-deletion pseudocount (*2.0*).

Insertion pseudocount (*0.02*).

No-insertion pseudocount (*1.0*).

Weight for generic versus
sequence-set-specific residue abundances ( *1e+99*).

Initial temperature (*1.2*).

Cooling factor per n iterations
(*1.44*).

Temperature lower bound (*0.1*).

Print progress information at each
iteration.

Column-sampling moves per site-sampling move
(*1.0*).

Site sampling algorithm: *0*=FAST
*1*=SLOW *2*=FFT (*0*).

Seed for pseudo-random numbers
(*1*).

- Author of GLAM2.

- Author of GLAM2.

- Formatted this manpage in DocBook XML for the Debian distribution.

05/19/2008 | GLAM2 1056 |