

                        DIVCLUS


Version.
   2.2.

Introduction.

References
   http://www.mrc-lmb.cam.ac.uk/genomes/divclus_home.html
   ftp.mrc-lmb.cam.ac.uk in the directory /pub/genomes/Geanfammer

Enclosed
   A biological sequence handling perl subroutine library is added.
   (B.pl)






#____________________________________________________________________________
# Title     : diviclus.pl
# Usage     : diviclus.pl xxxxx.msp [s=100][t=30][e=30][f=2][v]
#               or diviclus.pl *.msp
#                           -while xxx.msp is a file with MSP file format
#
# Function  : 1) merges similar sequences in MSP file fomrat making
#                hash output.
#             2) processes the merged msp contents to sort small things
#             3) connects the sequences when there is any common
#                region between preliminary clusters.
#             4) makes various files(xx.clu, xx.sat, xx.mrg) and
#                also shows in STDOUT.
#
#             To controll the division of clusters, play with
#              the below parameters(if you do not specify, defaults:
#               t=30, s=100, e=30, f=3
#              if you give them mulitiple fi,.es, it will process them
#              all together.
# Example   : diviclus.pl xxxxxx.msp s=90 t=40 e=10
#             Above is for score 90, seqlet leng 40, evalue 10.
#             However, usually you dont need options. Just put xxx.msp
#
# Keywords  : divide_clusters, diviclust, find_linker, subcluster
# Options   : _  for debugging.
#             #  for debugging.
#             r  for range attachment option
#             m  for merge file format(.mrg) output
#             v  for some info. printout, VERBOSE
#             S  for taking shorter region overlapped
#             L  for taking larger  region overlapped
#             A  for taking average region overlapped (default)
#
#  $short_region=  S by S -S # taking shorter region overlapped
#  $large_region=  L by L -L # taking larger  region overlapped
#  $average_region=A by A -A # taking average region overlapped
#  $verbose = v by v -v
#  $range = r by r -r
#  $merge = m by m -m
#  $sat_file = s by s -s
#  $dindom = d by d -d
#  $indup  = i by i -i
#  $over_write = w by w -w
#  $optimize   = o by o -o
#  $score = by s=    # Ssearch score cutoff, default 100
#  $factor = by f=   # factor is for the merge proces
#                      (misoverlap tolerance factor 3=33%, 2=50%)
#                      factor works within msp chunk for one sequence
#                      to filter a good mergable seqlets
#  $thresh = by t=   # seqlet length cutoff, default 30
#  $evalue = by e=   # maximum evalue cutoff default 30
#
# Author    : Sarah A. Teichmann and Jong Park
# Version   : 2.1
#------------------------------------------------------------------------------

