Read user-specified column weighting information.  This option requiresauxiliary data of the form:  Weights     list_of_weight_values    [per site, one or more lines]Example:  5  114  W  Weights     111111111111001100000100011111100000000000000110000110000000              111101111111111111111111011100000111001011100000000011  Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTG  ...It is necessary that the weight values not start before the 11'th character inthe line, or some of them will be lost.  Weights from 0 to 35 are indicated bythe series: 0, 1, 2, 3, ..., 9, A, B, ..., Y, Z.PHYLIP DNAML does not support user weights with values other than 1 or 0.This limit has been removed in fastDNAml to permit the use of user weightsas a mechanism for representing a bootstrap sample (that is, only theauxiliary data lines change, not the body of the data file).Y -- Write Tree  (*****  Changed in version 1.1  *****)fastDNAml writes the final tree to an output file called treefile.PID.  Bydefault the tree is in PHYLIP format.  The Y option allows turning this off,or changing the format of the tree.The Y option by itself toggles the saving of the tree, on or off.  If thereis also an auxiliary input line of the form:  Y numberwhere number can be 1, 2, or 3, the number selects one of three tree outputformats:  1  Newick  2  Prolog  3  PHYLIP (default)Newick is the tree standard used by PAUP, MacClade, and serveral otherprograms.  The tree includes a comment about the analysis that the tree isbased upon.  fastDNAml uses this comment when it reads a tree.  In addition,the names of the taxa are enclosed in quotation marks.  Both of thesefeatures of the file make it incompatible with the PHYLIP package.PHYLIP is the subset of the Newick tree standard used by programs in thePHYLIP package.  There are no comments and no quotations marks around names.(If a name includes unusual characters, such as a comma, fastDNAml will putit in quotation marks, making it a valid tree, but it cannot be read by thePHYLIP programs.)The Prolog format very similar to the Newick format, but it is a valid prologfact that permits direct loading into some sequence analysis tools that weuse.  The structure of the term is:  pseudo_newick([Comment], (Subtree1, Subtree2, Subtree3): Length).where each subtree is either  (Subtree1,Subtree2): Lengthor  Label: LengthThe comment is a valid prolog term when && is defined as a unary operator.Label is a prolog atom (it is a valid Newick label, with single quotationmarks).  Length is a number.Because the Y auxiliary input line is optional, it cannot be the last auxiliarydata line.Examples.  To turn of the saving of the tree,  5  114  Y  Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTG  ...or, to change the output to the full Newick format,  5  114  Y T  Y 1  T 2.0  Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTG  ...PHYLIP DNAML does not append the PID (process ID) to the tree file name anddoes not support the full Newick standard or the prolog format output.=============================================================================Acknowledgements:The origin and development of fastDNAml as a program to extend the use ofmaximum likelihood phylogenetic inference to larger sets of DNA sequenceswas encouraged by Carl Woese.  Through the development and evolution of theprogram, Joseph Felsenstein has been extremely helpful and encouraging.Numerous users have made suggestions and/or reported program bugs:   Gary Nunn   Tom Schmidt   Ross Overbeek   Hideo Matsuda   Mitchell Sogin   Brenden Rielly=============================================================================Examples:Data file with empirical frequencies (generic analysis) (notice that blanklines are permitted in the data):5  114Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCGData file with empirical frequencies and a random addition order:5  114  JJ 137Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCGData file with empirical frequencies and a bootstrap resampling:5  114  BB 137Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCGData with weighting mask and rate categories:5  114  W CWeights     111111111111001100000100011111100000000000000110000110000000            111101111111111111111111011100000111001011100000000011C  10  0.0625  0.125  0.25  0.5  1  2  4  8  16  32Categories  5111136343678975AAA8949995566778888889AAAAAA9239898629AAAAA9            633792246624457364222574877188898132984963499AA9899975Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCGData with three user-specified tree branching orders:5  114  USequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCG3(Sequence1,(Sequence2,Sequence3),(Sequence4,Sequence5));(Sequence2,(Sequence1,Sequence3),(Sequence4,Sequence5));(Sequence3,(Sequence1,Sequence2),(Sequence4,Sequence5));Data with transition/transversion ratio and base frequencies tosimulate Jukes & Cantor model:5  114  T FT 0.501F 0.25 0.25 0.25 0.25Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCGNon-interleaved data:5  114  ISequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCGNon-interleaved data by editing a GenBank format (make sure that the names arepadded to at least ten characters with blanks):5  114  ISequence1          1 ACACGGTGTC GTATCATGCT GCAGGATGCT AGACTGCGTC ANATGTTCGT ACTAACTGTG       61 AGCTCGATGA TCGGTGACGT AGACTCAGGG GCCATGCCGC GAGTTTGCGA TGCGSequence2          1 ACGCGGTGTC GTGTCATGCT ACATTATGCT AGACTGCGTC GGATGCTCGT ATTGACTGCG       61 AGCACGGTGA TCAATGACGT AGNCTCAGGR TCCACGCCGT GACTTTGTGA TNCGSequence3          1 ACGCGGTGCC GTGTNATGCT GCATTATGCT CGACTGCGRC GGATGCTAGT ATTGACTGCG       61 AGCACGATGA CCGATGACGT AGACTGAGGG TCCGTGCCGC GACTTTGTGA TGCGSequence4          1 ACGCGCTGCC GTGTCATCCT ACACGATGCY AGACAGCGTC AGCTGCTAGT ACTGGCTGAG       61 ACCTCGGTGA TTGATGACGT AGACTGCGGG TCCATGCCGC GATTTTGCGR TGCGSequence5          1 ACGCGCTGTC GTGTCATACT GCAGGATGCT AGACTGCGTC AGCTGCTAGT ACTGGCTGAG       61 ACCTCGATGC TCGATGACGT AGACTGCGGG TCCATGCCGT GATTTTGCGA TGCGData analysis restarted from a four-taxon tree (which happens to be wrong,but it will be corrected by local rearrangements after the tree is read):5  114  RSequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCG(Sequence4:0.1,Sequence2:0.1,(Sequence1:0.1,Sequence5:0.1):0.1):0.0;Data analysis restarted from a four-taxon tree (which is wrong, and whichwill not be corrected after the tree is read due to the suppression of allrearrangements by the global 0 0 option):5  114  R G TG 0 0T 2.0Sequence1   ACACGGTGTCGTATCATGCTGCAGGATGCTAGACTGCGTCANATGTTCGTACTAACTGTGSequence2   ACGCGGTGTCGTGTCATGCTACATTATGCTAGACTGCGTCGGATGCTCGTATTGACTGCGSequence3   ACGCGGTGCCGTGTNATGCTGCATTATGCTCGACTGCGRCGGATGCTAGTATTGACTGCGSequence4   ACGCGCTGCCGTGTCATCCTACACGATGCYAGACAGCGTCAGCTGCTAGTACTGGCTGAGSequence5   ACGCGCTGTCGTGTCATACTGCAGGATGCTAGACTGCGTCAGCTGCTAGTACTGGCTGAG            AGCTCGATGATCGGTGACGTAGACTCAGGGGCCATGCCGCGAGTTTGCGATGCG            AGCACGGTGATCAATGACGTAGNCTCAGGRTCCACGCCGTGACTTTGTGATNCG            AGCACGATGACCGATGACGTAGACTGAGGGTCCGTGCCGCGACTTTGTGATGCG            ACCTCGGTGATTGATGACGTAGACTGCGGGTCCATGCCGCGATTTTGCGRTGCG            ACCTCGATGCTCGATGACGTAGACTGCGGGTCCATGCCGTGATTTTGCGATGCG(Sequence4:0.1,Sequence2:0.1,(Sequence1:0.1,Sequence5:0.1):0.1):0.0;