Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_62 MOLecular PHYlogeny MOLPHY programs at MUSC.

The MOLPHY software was written by Jun Adachi & Masami Hasegawa 
Copyright (c) 1992-1994

There are several :
 
njdist -Neighbor Joining Phylogeny from Distance Matrix  
nucml  -Maximum Likelihood Inference of Nucleic Acid Phylogeny   
nucst  -Basic Statistics of Nucleic Acid Sequences  
protml -Maximum Likelihood Inference of Protein Phylogeny  
protst -Basic Statistics of Protein Sequences
totalml

Plus a lengthy series of utility PERL scripts for file data massage and 
format interconversion.

For MUSC users the most useful of these is "int2mol". This utility
converts an interleaved PHYLIP format( such as the output of the 
CLUSTALW program with the PHYLIP output option set) into a MOLPHY format. 
This MOLPHY formatted dataset may in turn be read by the PAML programs. 
  
ali2mol       
clus2mol
degene4
degene4l
disjoint
dna2ami
eali2mol
egetcds       
getcds       
ggetcds
infocode
infocode2 
inf2mol 
int2mol   -Interleaved -> MOLPHY
mega2mol      
molcut    -get partial sequences      
molcodon  -get 3rd(1st,2nd) codons
mol2phy   -MOLPHY -> Sequential     
molrev    -reverse DNA sequences
mol2int       
mollist   -get identifiers list
mol2mol   -MOLPHY format beautifer     
molmerge  -merge sequences
mol2seq       
molsplit
molcat   -concatenate sequences        
must2mol -MUST -> MOLPHY
mc2mol        
molcons
mol2inf       
molinfo  -get (non)infomation sites      
nuc2ptn        
nuc2NUC 
njt2tpl
nuc2code        
phy2mol  -Sequential -> MOLPHY
protmlA        
rmid3      
rminsdel  -remove INS/DEL sites      
rmleu                        
rmsyno         
seq2mol         
seqwrap
      
        

These are all programs with plain text 
user interfaces ( ie no fancy GUI).



     
 

The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
Last modified: June 2, 2000- ESH

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