							#############
							## utilCUB ## 
							#############
							
----------------------------------------------------------------
Copyright (c) 	Alain Viari & Eduardo Rocha
				Atelier de BioInformatique Universite Pierre et Marie Curie
@file: utilCUB.c					   
@desc: tabulate codon usage ENC ENCp S					   

---------------------------------------------------------------- 


------------------------------------------			
 utilCUB Version 0.1 June 09		
------------------------------------------			
synopsis :							
	Compute ENC (Effective Number of Codon) 
	ENC' (ENC with GC content correction) 
	and P (frequency of the optimal codons 
	for amino-acids Phe, Ile, Tyr and Asn) 

usage: utilCUB [-A freqA] [-C freqC] [-G freqG] [-c code] [-s] [-S] [-t]
------------------------------------------			
options:							

	-h   : [H]elp - print <this> help			
  	-A   : frequency of A
  	-C   : frequency of C
  	-G   : frequency of G
  	-c code
      0 : universal
      1 : mito yeast
      2 : mito vertebrate
      3 : filamentous fungi
      4 : mito insects & platyhelminthes
      5 : Candida cylindracea
      6 : Ciliata
      7 : Euplotes
      8 : mito echinoderms
  	-s       : ignore first (start) codon
  	-S       : ignore last  (stop)  codon
  	-t       : test if there is a stop and if so ignore 
------------------------------------------			
file formats															
seqfile:  DNA fasta format sequences length multiple of 3 
------------------------------------------

							#################
							## util_tab_aa ## 
							#################
							
----------------------------------------------------------------
Copyright (c) 	Alain Viari & Eduardo Rocha
				Atelier de BioInformatique Universite Pierre et Marie Curie
@file: util_tab_aa.c						   
@desc: tabulate amino acid usage					   

---------------------------------------------------------------- 

------------------------------------------			
 util_tab_aa Version 2001					
------------------------------------------			
synopsis :
tabulate amino-acid usage

usage: util_tab_aa [-1] [-i alpha] [-x]
------------------------------------------
   -1       : ignore first residue
   -i alpha : ignore symbols in alpha
   -r       : compute relative frequencies
   -t       : print last total line
   -x       : ignore unknown symbol
------------------------------------------
file formats							
								
 seqfile       :  fasta format				
------------------------------------------


							###############
							## getentryF ## 
							###############

----------------------------------------------------------------
Copyright (c) 	Alain Viari & Eduardo Rocha
				Atelier de BioInformatique Universite Pierre et Marie Curie
@file: getentryF_main.c					   
@desc: retrieves sequences by list of identifiers					   

---------------------------------------------------------------- 


------------------------------------------			
 getentryF Version 0.1 Sept 09					
------------------------------------------			
synopsis :							
  gets entries in a database from a file with ids 
								
usage: getentry [options] db_file					
------------------------------------------			
options:							
-h           : [H]elp - print <this> help			
-c string    : case insensitive	
-f string    : file with ids (one per line)	
------------------------------------------			
file formats							
db_file:        fasta format					
 if n > MAX_SEQ it outputs an error 
--------------------------------				
				

							###############
							## translate ## 
							###############

----------------------------------------------------------------
Copyright (c) 	Alain Viari & Eduardo Rocha
				Atelier de BioInformatique Universite Pierre et Marie Curie
@file: translate.c					   
@desc: translate a fasta nucleic sequence					   

---------------------------------------------------------------- 

------------------------------------------			
 translate Version 1.3 Sep 06			
------------------------------------------			
synopsis :							
  gets gene sequences and translates to protein 
								
 usage: translate [-c (0-8)] [-s] [-S] seq.file				
------------------------------------------			
options:							
 -h          : [H]elp - print <this> help			
 -c code     :  
             : 0 - universal 
             : 1 - mito yeast 
             : 2 - mito vertebrate 
             : 3 - filamentous fungi & Mycoplasma 
             : 4 - mito insects & platyhelminthes 
             : 5 - Candida cylindracea 
             : 6 - Ciliata 
             : 7 - Euplotes 
             : 8 - mito echinoderms 
 -p          : remove Met as Map does 
 -f          : reject if there are inner stops (frameshifts) 
 -m          : force Met as start codon if [AGT]TG 
             : note: incompatible with -s & -M 
 -M          : really force start to be Met 
             : note: incompatible with -s & -m
 -s          : ignore first (start) codon 
             : note: incompatible with -m & -M
 -S          : ignore last  (stop)  codon 
------------------------------------------			
file formats							
								
 seqfile       :  fasta format				
--------------------------------

