Provided by: melting_4.3.1+dfsg-1_amd64 bug

NAME

       melting - nearest-neighbor computation of nucleic acid hybridation

SYNOPSIS

       melting [options]

DESCRIPTION

       Melting  computes,  for  a nucleic acid duplex, the enthalpy and the entropy of the helix-
       coil transition, and then its melting  temperature.   Three  types  of  hybridisation  are
       possible:  DNA/DNA,  DNA/RNA,  and  RNA/RNA.   The  program  uses  the  method of nearest-
       neighbors. The set of  thermodynamic  parameters  can  be  easely  changed,  for  instance
       following  an  experimental  breakthrough.  Melting is a free program in both sense of the
       term. It comes with no cost and it is open-source. In addition it is coded in  ISO  C  and
       can  be  compiled  on  any  operating  system.  Some perl scripts are provided to show how
       melting can be used as a block to construct more ambitious programs.

OPTIONS

       The options are treated sequentially. If there is a conflict  between  the  value  of  two
       options, the latter normally erases the former.

       -Afile.nn
              Informs  the  program  to  use  file.nn  as  an alternative set of nearest-neighbor
              parameters, rather than the default  for  the  specified  hybridisation  type.  The
              standard  distribution  of  melting  provides  some  files  ready-to-use: all97a.nn
              (Allawi et al 1997), bre86a.nn (Breslauer et al 1986), san96a.nn (SantaLucia et  al
              1996), sug96a.nn (Sugimoto et al 1996) san04a.nn (Santalucia et al 2004) (DNA/DNA),
              fre86a.nn (Freier et al 1986), xia98a.nn (Xia et al 1998), (RNA/RNA), and sug95a.nn
              (Sugimoto et al 1995), (DNA/RNA).

              The   program  will  look  for  the  file  in  a  directory  specified  during  the
              installation. However, if an environment variable NN_PATH is defined, melting  will
              search  in  this one first. Be careful, the option -A changes the default parameter
              set defined by the option -H.

       -Ccomplementary_sequence
              Enters the complementary sequence, from 3' to 5'. This option is mandatory if there
              are mismatches between the two strands. If it is not used, the program will compute
              it as the complement of the sequence entered with the option -S.

       -Ddnadnade.nn
              Informs the program to use the file dnadnade.nn  to  compute  the  contribution  of
              dangling  ends to the thermodynamic of helix-coil transition. The dangling ends are
              not taken into account by the approximative mode.

       -Ffactor
              This is the a correction factor used to modulate the effect of  the   nucleic  acid
              concentration  in the computation of the melting temperature. See section ALGORITHM
              for details.

       -Gx.xxe-xx
              Magnesium  concentration  (No maximum concentration for the moment). The effect
                 of  ions  on  thermodynamic  stability  of nucleic  acid duplexes is complex,
                 and the correcting functions are  at  best rough  approximations.The published
                 Tm  correction formula for divalent Mg2+ ions of  Owczarzy  et al(2008) can
                 take in account the competitive binding of monovalent and divalent ions on DNA.
                 However this formula is only for DNA duplexes.

       -h     Displays a short help and quit with EXIT_SUCCESS.

       -Hhybridisation_type
              Specifies the hybridisation type. This will set the nearest-neighbor set to use  if
              no  alternative  set  is  provided  by the option -A (remember the options are read
              sequentially). Moreover this parameter  determines  the  equation  to  use  if  the
              sequence  length  exceeds the limit of application of the nearest-neighbor approach
              (arbitrarily set up by the author). Possible values are dnadna, dnarna  and  rnadna
              (synonymous),  and rnarna.  For reasons of compatibility the values of the previous
              versions  of  melting  A,B,C,F,R,S,T,U,W  are  still  available  although  strongly
              deprecated.  Use  the  option  -A  to  require  an alternative set of thermodynamic
              parameters. IMPORTANT: If the duplex is a DNA/RNA heteroduplex, the sequence of the
              DNA strand has to be entered with the option -S.

       -Iinput_file
              Provides  the name of an input file containing the parameters of the run. The input
              has to contain one parameter per line, formatted as in the command line. The  order
              is not important, as well as blank lines. example:

              ###beginning###
              -Hdnadna
              -Asug96a.nn
              -SAGCTCGACTC
              -CTCGAGGTGAG
              -N0.2
              -P0.0001
              -v
              -Ksan96a

              ###end###

       -ifile.nn
                Informs  the  program to use file.nn as an alternative set  of  inosine pair
                parameters, rather than  the  default  for the specified hybridisation type.
                The   standard   distribution  of  melting  provides  some   files  ready-to-use:
              san05a.nn
               (Santalucia et al 2005) for deoxyinosine  in  DNA  duplexes,  bre07a.nn  (Brent  M
              Znosko
                et  al  2007)for  inosine  in  RNA  duplexes.  Note   that   not  all the inosine
              mismatched
                wobble's pairs have been  investigated.  Therefore  it  could  be  impossible  to
              compute
                the  Tm  of  a  duplex  with inosine pairs. Moreover, those inosine pairs are not
              taken
                into account by the  approximative mode.

       -Ksalt_correction
              Permits to chose another correction for the concentration in sodium. Currently, one
              can  chose  between  wet91a, san96a, san98a.  See section ALGORITHM.  TP.  BI. "-k"
              "x.xxe-xx"
                 Potassium  concentration  (No maximum concentration for the moment). The  effect
              of ions
                 on   thermodynamic   stability   of  nucleic   acid duplexes is complex, and the
              correcting
                 functions are  at  best  rough   approximations.The  published   Tm   correction
              formula for
                 sodium  ions  of  Owczarzy  et  al (2008)is therefore also applicable to buffers
              containing Tris or
                 KCl. Monovalent K+, Na+, Tris+ ions  stabilize  DNA duplexes
                 with similar potency, and  their  effects  on  duplex  stability  are  additive.
              However this formula
                 is only for DNA duplexes.

       -L     Prints the legal informations and quit with EXIT_SUCCESS.

       -Mdnadnamm.nn
              Informs  the  program  to  use  the file dnadnamm.nn to compute the contribution of
              mismatches to the thermodynamic of helix-coil transition. Note  that  not  all  the
              mismatched  Crick's  pairs have been investigated. Therefore it could be impossible
              to compute the Tm of a mismatched duplex. Moreover, those mismatches are not  taken
              into account by the approximative mode.

       -Nx.xxe-xx
              Sodium concentration (between 0 and 10 M). The effect of ions on thermodynamic
                stability of nucleic acid duplexes is complex, and the correcting functions
                are at best rough approximations. Moreover, they are generally reliable only
                for [Na+] belonging to [0.1,10M]. If there are no other ions in
                solution,  we  can  use only the sodium correction. In the other case, we use the
              Owczarzy's
                algorithm.

       -Ooutput_file
              The output is directed to this file instead of the standard output. The name of the
              file   can   be  omitted.  An  automatic  name  is  then  generated,  of  the  form
              meltingYYYYMMMDD_HHhMMm.out (of course, on POSIX compliant systems, you can emulate
              this with the redirection of stdout to a file constructed with the program date).

       -Px.xxe-xx
              Concentration of the nucleic acid strand in excess (between 0 and 0.1 M).

       -p     Return  the  directory  supposed to contain the sets of calorimetric parameters and
              quit with EXIT_SUCCESS. If the environment variable NN_PATH is set, it is returned.
              Otherwise, the value defined by default during the compilation is returned.

       -q     Turn  off  the  interactive correction of wrongly entered parameter. Useful for run
              through a server, or a batch script. Default is  OFF  (i.e.  interactive  on).  The
              switch  works in both sens.  Therefore if -q has been set in an input file, another
              -q on the command line will switch the quiet mode OFF (same thing if two -q are set
              on the same command line).

       -Ssequence
              Sequence  of one strand of the nucleic acid duplex, entered 5' to 3'. IMPORTANT: If
              it is a DNA/RNA heteroduplex, the sequence of the DNA strand  has  to  be  entered.
              Uridine  and  thymidine  are  considered  as  identical.  The bases can be upper or
              lowercase.

       -Txxx  Size threshold before approximative  computation.  The  nearest-neighbour  approach
              will be used only if the length of the sequence is inferior to this threshold.

       -tx.xxe-xx
              Tris buffer  concentration  (No maximum concentration for the moment).
                 The effect  of  ions  on  thermodynamic  stability  of nucleic  acid
                 duplexes is complex, and the correcting functions are  at  best
                 rough  approximations.The published  Tm  correction formula for sodium ions of
                 Owczarzy et al(2008)is therefore also applicable to buffers containing Tris or
                 KCl.  Monovalent  K+,  Na+,  Tris+  ions   stabilize   DNA duplexes with similar
              potency, and
                 their effects on duplex stability are additive. However this formula is only for
              DNA
                 duplexes.  Be  careful,  the  Tris+ ion concentration is about half of the total
              tris buffer
                 concentration.

       -v     Control the verbose mode, issuing a lot more information about the current run (try
              it  once  to  see if you can get something interesting). Default is OFF. The switch
              works in both sens. Therefore if -v has been set in an input file,  another  -v  on
              the  command line will switch the verbose mode OFF (same thing if two -v are set on
              the same command line).

       -V     Displays the version number and quit with EXIT_SUCCESS.

       -x     Force the program to compute an approximative tm, based on G+C content. This option
              has to be used with caution. Note that such a calcul is increasingly incorrect when
              the length of the duplex decreases. Moreover, it does not take into account nucleic
              acid concentration, which is a strong mistake.

ALGORITHM

   Thermodynamics of helix-coil transition of nucleic acid
       The nearest-neighbor approach is based on the fact that the helix-coil transition works as
       a  zipper.   After  an  initial  attachment,  the  hybridisation   propagates   laterally.
       Therefore,  the  process  depends  on the adjacent nucleotides on each strand (the Crick's
       pairs).  Two duplexes with the same base pairs could have different  stabilities,  and  on
       the  contrary,  two  duplexes with different sequences but identical sets of Crick's pairs
       will have the same thermodynamics properties (see Sugimoto et  al.  1994).   This  program
       first  computes  the  hybridisation enthalpy and entropy from the elementary parameters of
       each Crick's pair.

       DeltaH = deltaH(initiation) + SUM(deltaH(Crick's pair))
       DeltaS = deltaS(initiation) + SUM(deltaS(Crick's pair))

       See Wetmur J.G. (1991) and  SantaLucia  (1998)  for  deep  reviews  on  the  nucleic  acid
       hybridisation and on the different set of nearest-neighbor parameters.

   Effect of mismatches and dangling ends
       The  mismatching  pairs  are also taken into account. However the thermodynamic parameters
       are still not available  for  every  possible  cases  (notably  when  both  positions  are
       mismatched). In such a case, the program, unable to compute any relevant result, will quit
       with a warning.

       The two first and  positions  cannot  be  mismatched.  in  such  a  case,  the  result  is
       unpredictable,  and  all  cases are possible. for instance (see Allawi and SanLucia 1997),
       the duplex

       A          T
        GTGAGCTCAT
        TACTCGAGTG
       T          A

       is more stable than

       AGTGAGCTCATT
       TTACTCGAGTGA

       The dangling ends, that is the umatched terminal nucleotides, can be taken into account.

   Example
       DeltaH(
       AGCGATGAA-
       -CGCTGCTTT
       ) = DeltaH(AG/-C)+DeltaH(A-/TT)
       +DeltaH(initG/C)+DeltaH(initA/T)
       +DeltaH(GC/CG)+DeltaH(CG/GC)+2xDeltaH(GA/CT)+DeltaH(AA/TT)
       +Delta(AT/TG mismatch) +DeltaG(TC/GG mismatch)

       (The same computation is performed for DeltaS)

   The melting temperature
       Then the melting temperature is computed by the following formula:

       Tm = DeltaH / (DeltaS + Rx ln ([nucleic acid]/F))
       Tm in K (for [Na+] = 1 M )
            + f([Na+]) - 273.15
       correction  for  the  salt  concentration  (if  there  are  only  sodium  cations  in  the
       solution)and  to  get  the  temperature  in degree Celsius.  (In fact some corrections are
       directly included in the DeltaS see that of SanLucia 1998)

   Correction for the concentration of nucleic acid
       If the concentration of the two strands are similar, F is 1 in case of  self-complementary
       oligonucleotides,  4  otherwise.  If  one  strand  is  in  excess  (for  instance  in  PCR
       experiment),  F  is  2  (Actually  the  formula  would  have  to  use  the  difference  of
       concentrations  rather  than the total concentration, but if the excess is sufficient, the
       total concentration can be assumed to be identical to the concentration of the  strand  in
       excess).

       Note however, MELTING makes the assumption of no self-assembly, i.e.  the computation does
       not take any entropic term to correct for self-complementarity.

   Correction for the concentration of salt
       If there are only sodium ions in the solution, we can use the following corrections:

       The correction can be chosen between wet91a, presented in Wetmur 1991 i.e.
       16.6 x log([Na+] / (1 + 0.7 x [Na+])) + 3.85

       san96a presented in SantaLucia et al. 1996 i.e.
       12.5 x log[Na+]

       and san98a presented in SantaLucia 1998 i.e.  a correction of the  entropic  term  without
       modification of enthalpy
       DeltaS = DeltaS([Na+]=1M) + 0.368 x (N-1) x ln[Na+]

       Where  N is the length of the duplex (SantaLucia 1998 actually used 'N' the number of non-
       terminal phosphates, that is effectively equal to our N-1). CAUTION,  this  correction  is
       meant to correct entropy values expressed in cal.mol-1.K-1!!!

   Correction  for  the  concentration of ions when other monovalent ions such as Tris+ and K+ or
       divalent Mg2+ ions are added
       If there are only Na+ ions, we can use the correction for the  concentration  of  salt(see
       above).  In  the  opposite case , we will use the magnesium and monovalent ions correction
       from Owczarzy et al (2008). (only for DNA duplexes)

       [Mon+] = [Na+] + [K+] + [Tris+]

       Where [Tris+] = [Tris buffer]/2. (in the option -t, it is the  Tris  buffer  concentration
       which is entered).

       If [Mon+] = 0, the divalent ions are the only ions present
        and the melting temperature is :

       1/Tm(Mg2+) = 1/Tm(1M Na+) + a - b x ln([Mg2+]) + Fgc x (c + d x ln([Mg2+]) + 1/(2 x (Nbp -
       1)) x (- e +f x ln([Mg2+]) + g x ln([Mg2+]) x ln([Mg2+]))

       where : a = 3.92/100000.  b = 9.11/1000000.  c =  6.26/100000.   d  =  1.42/100000.   e  =
       4.82/10000.   f  =  5.25/10000.  g = 8.31/100000.  Fgc is the fraction of GC base pairs in
       the sequence and Nbp is the length of the sequence (Number of base pairs).

       If [Mon+] > 0, there are several cases because we  can  have  a  competitive  DNA  binding
       between monovalent and divalent cations  :

       If  the  ratio  [Mg2+]^(0.5)/[Mon+]  is  inferior  to  0.22,  monovalent  ion influence is
       dominant, divalent cations can be disregarded and the melting temperature is :

       1/Tm(Mg2+) = 1/Tm(1M Na+) + (4.29 x Fgc - 3.95) x 1/100000 x ln([mon+]) + 9.40 x 1/1000000
       x ln([Mon+]) x ln([Mon+])

       where : Fgc is the fraction of GC base pairs in the sequence.

       If  the  ratio  [Mg2+]^(0.5)/[Mon+] is included in [0.22, 6[, we must take in account both
       Mg2+ and monovalent cations concentrations. The melting temperature is :

       1/Tm(Mg2+) = 1/Tm(1M Na+) + a - b x ln([Mg2+]) + Fgc x (c + d x ln([Mg2+]) + 1/(2 x (Nbp -
       1)) x (- e + f x ln([Mg2+]) + g x ln([Mg2+]) x ln([Mg2+]))

       where : a = 3.92/100000 x (0.843 - 0.352 x [Mon+]0.5 x ln([Mon+])).
               b = 9.11/1000000.       c = 6.26/100000.
               d  =  1.42/100000 x (1.279 - 4.03/1000 x ln([mon+]) - 8.03/1000 x      ln([mon+] x
       ln([mon+]).       e = 4.82/10000.       f = 5.25/10000.       g = 8.31/100000 x  (0.486  -
       0.258 x ln([mon+]) + 5.25/1000 x ln([mon+] x ln([mon+] x ln([mon+]).

       Fgc is the fraction of GC base pairs in the sequence and Nbp is the length of the sequence
       (Number of base pairs).

       Finally, if the ratio [Mg2+]^(0.5)/[Mon+] is superior to  6,  divalent  ion  influence  is
       dominant, monovalent cations can be disregarded and the melting temperature is :

       1/Tm(Mg2+) = 1/Tm(1M Na+) + a - b x ln([Mg2+]) + Fgc x (c + d x ln([Mg2+]) + 1/(2 x (Nbp -
       1)) x (- e + f x ln([Mg2+]) + g x ln([Mg2+]) x ln([Mg2+]))

       where : a = 3.92/100000.  b = 9.11/1000000.  c =  6.26/100000.   d  =  1.42/100000.   e  =
       4.82/10000.  f = 5.25/10000.  g = 8.31/100000.

       Fgc is the fraction of GC base pairs in the sequence and Nbp is the length of the sequence
       (Number of base pairs).

   Long sequences
       It is important to realise that the nearest-neighbor  approach  has  been  established  on
       small  oligonucleotides.  Therefore  the  use  of melting in the non-approximative mode is
       really accurate only for relatively short sequences (Although if  the  sequences  are  two
       short,  let's  say  <  6  bp,  the  influence of extremities becomes too important and the
       reliability decreases a lot). For long sequences an approximative mode has been  designed.
       This  mode is launched if the sequence length is higher than the value given by the option
       -T (the default threshold is 60 bp).

       The melting temperature is computed by the following formulas:

       DNA/DNA:
       Tm = 81.5+16.6*log10([Na+]/(1+0.7[Na+]))+0.41%GC-500/size

       DNA/RNA:
       Tm = 67+16.6*log10([Na+]/(1.0+0.7[Na+]))+0.8%GC-500/size

       RNA/RNA:
       Tm = 78+16.6*log10([Na+]/(1.0+0.7[Na+]))+0.7%GC-500/size

       This mode is nevertheless strongly disencouraged.

   Miscellaneous comments
       Melting is currently accurate only when the hybridisation is performed at pH 71.

       The computation is  valid  only  for  the  hybridisations  performed  in  aqueous  medium.
       Therefore  the  use  of  denaturing  agents  such  as formamide completely invalidates the
       results.

REFERENCES

       Allawi H.T., SantaLucia J. (1997).  Thermodynamics and NMR of internal G.T  mismatches  in
       DNA.  Biochemistry 36: 10581-10594

       Allawi  H.T.,  SantaLucia  J.  (1998).   Nearest  Neighbor  thermodynamics  parameters for
       internal G.A mismatches in DNA.  Biochemistry 37: 2170-2179

       Allawi H.T., SantaLucia J. (1998).  Thermodynamics of  internal  C.T  mismatches  in  DNA.
       Nucleic Acids Res 26: 2694-2701.

       Allawi  H.T.,  SantaLucia  J.  (1998).   Nearest  Neighbor  thermodynamics of internal A.C
       mismatches in DNA: sequence dependence and pH effects.  Biochemistry 37: 9435-9444.

       Bommarito S., Peyret N., SantaLucia J. (2000).  Thermodynamic parameters for DNA sequences
       with dangling ends.  Nucleic Acids Res 28: 1929-1934

       Breslauer K.J., Frank R., Bl�ker H., Marky L.A. (1986).  Predicting DNA duplex stability
       from the base sequence.  Proc Natl Acad Sci USA 83: 3746-3750

       Freier S.M., Kierzek R., Jaeger J.A., Sugimoto N., Caruthers M.H., Neilson T., Turner D.H.
       (1986).   Improved  free-energy  parameters  for  predictions  of  RNA  duplex  stability.
       Biochemistry 83:9373-9377

       Owczarzy R., Moreira B.G., You Y., Behlke M.B., Walder J.A.  (2008)  Predicting  stability
       of DNA duplexes in solutions containing Magnesium and Monovalent Cations. Biochemistry 47:
       5336-5353.

       Peyret N.,  Seneviratne  P.A.,  Allawi  H.T.,  SantaLucia  J.  (1999).   Nearest  Neighbor
       thermodynamics  and  NMR  of DNA sequences with internal A.A, C.C, G.G and T.T mismatches.
       dependence and pH effects.  Biochemistry 38: 3468-3477

       SantaLucia J.  Jr,  Allawi  H.T.,  Seneviratne  P.A.  (1996).   Improved  nearest-neighbor
       parameters for predicting DNA duplex stability.  Biochemistry 35: 3555-3562

       Sugimoto  N.,  Katoh M., Nakano S., Ohmichi T., Sasaki M. (1994).  RNA/DNA hybrid duplexes
       with identical nearest-neighbor base-pairs hve identical  stability.   FEBS  Letters  354:
       74-78

       Sugimoto  N.,  Nakano  S.,  Katoh  M., Matsumura A., Nakamuta H., Ohmichi T., Yoneyama M.,
       Sasaki M. (1995).   Thermodynamic  parameters  to  predict  stability  of  RNA/DNA  hybrid
       duplexes.  Biochemistry 34: 11211-11216

       Sugimoto  N.,  Nakano S., Yoneyama M., Honda K. (1996).  Improved thermodynamic parameters
       and helix initiation factor to predict stability of  DNA  duplexes.   Nuc  Acids  Res  24:
       4501-4505

       Watkins  N.E., Santalucia J. Jr. (2005). Nearest-neighbor t- hermodynamics of deoxyinosine
       pairs in DNA duplexes. Nucleic Acids Research 33: 6258-6267

       Wright D.J., Rice J.L., Yanker D.M., Znosko B.M. (2007).  Nearest neighbor parameters  for
       inosine-uridine pairs in RNA duplexes. Biochemistry 46: 4625-4634

       Xia  T.,  SantaLucia J., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox C., Turner
       D.H. (1998).   Thermodynamics  parameters  for  an  expanded  nearest-neighbor  model  for
       formation of RNA duplexes with Watson-Crick base pairs.  Biochemistry 37: 14719-14735

       For review see:

       SantaLucia J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-
       neighbor thermodynamics.  Proc Natl Acad Sci USA 95: 1460-1465

       SantaLucia  J., Hicks Donald (2004) The Thermodynamics of  DNA  structural  motifs.  Annu.
       Rev. Biophys. Struct. 33: 415 -440

       Wetmur   J.G.   (1991)  DNA  probes:  applications  of  the  principles  of  nucleic  acid
       hybridization.  Crit Rev Biochem Mol Biol 26: 227-259

FILES

       *.nn   Files containing the nearest-neighbor parameters, enthalpy and  entropy,  for  each
              Crick's pair.  They have to be placed in a directory defined during the compilation
              or targeted by the environment variable NN_PATH.

       tkmelting.pl
              A Graphical User Interface written in Perl/Tk is available for those who prefer the
              'button and menu' approach.

       *.pl   Scripts are available to use MELTING iteratively. For instance, the script multi.pl
              permits to predict the Tm of several duplexes in one  shot.  The  script  profil.pl
              allow an interactive computation along a sequence, by sliding a window of specified
              width.

SEE ALSO

       New versions and related material can be found  at  http://www.ebi.ac.uk/compneur/melting/
       and at at https://sourceforge.net/projects/melting/

KNOWN BUGS

       The  infiles  have  to  be  ended  by  a blank line because otherwise the last line is not
       decoded.

       If an infile is called, containing the address of another input file, it does not care  of
       this latter.  If it is its own address, the program quit (is it a bug or a feature?).

       In interactive mode, a sequence can be entered on several lines with a backslash

       AGCGACGAGCTAGCCTA\
       AGGACCTATACGAC

       If by mistake it is entered as

       AGCGACGAGCTAGCCTA\AGGACCTATACGAC

       The backslash will be considered as an illegal character. Here again, I do not think it is
       actually a bug (even if it is unlikely, there is a small probability  that  the  backslash
       could actually be a mistyped base).

COPYRIGHT

       Melting is copyright (C) 1997, 2013 by Nicolas Le Novère and Marine Dumousseau

       This program is free software; you can redistribute it and/or modify it under the terms of
       the GNU General Public License as  published  by  the  Free  Software  Foundation;  either
       version 2 of the License, or (at your option) any later version.

       This  program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
       without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR  PURPOSE.
       See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program;
       if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite  330,  Boston,
       MA  02111-1307 USA

ACKNOWLEDGEMENTS

       Nicolas  Joly is an efficient and kind debugger and advisor.  Catherine Letondal wrote the
       HTML interface to melting. Thanks to Nirav Merchant, Taejoon Kwon,  Leo  Schalkwyk,  Mauro
       Petrillo,  Andrew  Thompson,  Wong Chee Hong, Ivano Zara for their bug fixes and comments.
       Thanks to Richard Owczarzy for his magnesium correction. Thanks to Charles Plessy for  the
       graphical  interface  files.   Markus  Piotrowski  updated TkMELTING to cover version 4.3.
       Finally thanks to the usenet helpers, particularly Olivier Dehon and Nicolas Chuche.

AUTHORS

       Nicolas Le Novère Babraham Institute, Babraham Research Campus Babraham CB22 3AT Cambridge
       United-Kingdom.  n.lenovere@gmail.com

       Marine  Dumousseau  EMBL-EBI,  Wellcome-Trust  Genome  Campus  Hinxton  CB10 1SD Cambridge
       United-Kingdom.  marine@ebi.ac.uk

HISTORY

       See the file ChangeLog for the changes of the versions 4 and more recent.