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Bio::Clustalw::MultipleAlignCL Class Reference

List of all members.


Detailed Description

Represent a clustalw multiple alignment command line.

This is meant to make it easy to code the command line options you
want to submit to clustalw.

Clustalw has a ton of options and things to do but this is set up to
represent a clustalw mutliple alignment.

Warning: I don't use all of these options personally, so if you find
one to be broken for any reason, please let us know!

Definition at line 296 of file __init__.py.


Public Member Functions

def __init__
def __str__
def set_dna_matrix
def set_guide_tree
def set_new_guide_tree
def set_output
def set_protein_matrix
def set_type

Public Attributes

 add_seqnos
 allow_negative
 change_case
 command
 dna_matrix
 gap_ext_pen
 gap_open_pen
 gap_sep_range
 guide_tree
 h_gap_residues
 is_no_end_pen
 is_no_hgap
 is_no_pgap
 is_quick
 max_div
 new_tree
 output_file
 output_order
 output_type
 protein_matrix
 sequence_file
 trans_weight
 type

Static Public Attributes

list DNA_MATRIX = ['IUB', 'CLUSTALW']
list OUTPUT_CASE = ['LOWER', 'UPPER']
list OUTPUT_ORDER = ['INPUT', 'ALIGNED']
list OUTPUT_SEQNOS = ['OFF', 'ON']
list OUTPUT_TYPES = ['GCG', 'GDE', 'PHYLIP', 'PIR', 'NEXUS', 'FASTA']
list PROTEIN_MATRIX = ['BLOSUM', 'PAM', 'GONNET', 'ID']
list RESIDUE_TYPES = ['PROTEIN', 'DNA']

The documentation for this class was generated from the following file:

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