Bio::Tools::Run::PiseApplication::align2model 1.4

Bio::Tools::Run::PiseApplication::align2model is a Bioperl class for align2model - create a multiple alignment of sequences to an existing model.

Parameters:

align2model (String)

run (String)
Run name

db (Sequence)
Sequences to align (-db)

model_file (InFile)
Model (-i)
pipe: sam_model

id (String)
Sequence identifier(s) selection (separated by commas) (-id)

nscoreseq (Integer)
Maximum number of sequences to be read (-nscoreseq)

adpstyle (Excl)
Dynamic programming style (-adpstyle

SW (Excl)
Sequence scoring (-SW)

auto_fim (Switch)
Add FIMs automatically (-auto_fim)

jump_in_prob (Float)
Probability cost of jumping into the center of the model (-jump_in_prob)

jump_out_prob (Float)
Probability cost of jumping out the center of the model (-jump_out_prob)

a2mdots (Switch)
Print dots to fill space need for other sequences insertions (-a2mdots)

dump_parameters (Excl)
(-dump_parameters)