Trees | Index | Help |
---|
Package Bio :: Package Nexus :: Module Nexus |
|
Classes | |
---|---|
Block |
Represent a NEXUS block with block name and list of commandlines . |
CharBuffer |
Helps reading NEXUS-words and characters from a buffer. |
Commandline |
Represent a commandline as command and options. |
Nexus |
|
StepMatrix |
Calculate a stepmatrix for weighted parsimony. |
Exceptions | |
---|---|
NexusError |
Function Summary | |
---|---|
Combine matrices in [(name,nexus-instance),...] and return new nexus instance. | |
Return position of first and last character which is not in skiplist (defaults to ['-','?']). | |
Remove quotes and/or double quotes around identifiers. | |
Return a taxon identifier according to NEXUS standard. |
Function Details |
---|
combine(matrices)Combine matrices in [(name,nexus-instance),...] and return new nexus instance. combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...] Character sets, character partitions and taxon sets are prefixed, readjusted and present in the combined matrix. |
get_start_end(sequence, skiplist=['-', '?'])Return position of first and last character which is not in skiplist (defaults to ['-','?']). |
quotestrip(word)Remove quotes and/or double quotes around identifiers. |
safename(name, mrbayes=False)Return a taxon identifier according to NEXUS standard. Wrap quotes around names with punctuation or whitespace, and double single quotes. mrbayes=True: write names without quotes, whitespace or punctuation for mrbayes. |
Trees | Index | Help |
---|
Generated by Epydoc 2.1 on Wed Jan 31 09:58:01 2007 | http://epydoc.sf.net |