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       prequel - Compute marginal probability distributions for bases at ancestral


       Compute  marginal probability distributions for bases at ancestral nodes in a phylogenetic
       tree, using the tree model defined in tree.mod (may be  produced  with  phyloFit).   These
       distributions  are  computed  using  the  sum-product  algorithm, assuming independence of

       Currently, indels  are  not  treated  probabilistically  (hence  the  "largely")  but  are
       reconstructed  by  parsimony, also assuming site independence.  Specifically, each base is
       assumed to have been inserted on the branch leading to the last common ancestor  (LCA)  of
       all  species  that  have  actual bases (as opposed to alignment gaps or missing data) at a
       given site; gaps in descendant species are assumed to have  arisen  (parsimoniously)  from
       deletions.  When this LCA is either the left or right child of the root, insertions on one
       branch cannot be distinguished from deletions on the other.  We conservatively assume that
       the  base  was  present  at  the  root and was subsequently deleted.  (Note that this will
       produce an upward bias on the length of the sequence at the root.)  Output is to files  of
       the form outroot.XXX.probs, where XXX is the name of an ancestral node in the tree.  These
       nodes may be named explicitly in tree.mod.  Any ancestral node that is left  unnamed  will
       be  given  a  name that is a concatenation of two names, belonging to arbitrarily selected
       leaves of each subtree beneath the node (see below).


       Given a multiple alignment  in  a  file  called  "mammals.fa"  and  a  tree  model  called
       "mytree.mod" (see phyloFit), reconstruct all ancestral sequences:

              prequel mammals.fa mytree.mod anc

       If the TREE definition in mytree.mod has labeled ancestral nodes, e.g.,


       then   output   will  be  to  files  named  "anc.primate.probs",  "anc.rodent.probs",  and
       "anc.mammal.probs".  (See
       If instead the ancestral nodes are unlabeled, e.g.,


       then names will be created by concatenating  leaf  names,  e.g.,  "anc.human-chimp.probs",
       "anc.mouse-rat.probs", and "anc.human-mouse.probs".

       Each  output file will consist of a row for each position in the sequence and a column for
       each base, with the (i,j)th value giving the probability of base j  at  position  i.   For


              p(C)    p(G)    p(T)


              0.000039        0.998460        0.000052


              0.000065        0.001755        0.000030


              0.271307        0.000599        0.727668


              0.000039        0.998460        0.000052


              0.000179        0.973813        0.000182


       By default, no row is reported for bases inferred not to have been present at an ancestral
       node, so the number of rows will generally be smaller than the number of  columns  in  the
       input alignment.  However, if you wish to maintain a correspondence between row number and
       alignment column, you can use the --keep-gaps option, which will cause "padding"  rows  to
       be included in the output, e.g.,


              p(C)    p(G)    p(T)


              0.000065        0.001755        0.000030


              0.000039        0.998460        0.000052


              0.000393        0.873431        0.000365




              0.004878        0.018097        0.118851        0.858174

              0.000030        0.001637        0.000064        0.998269


       The  output  files  produced  by  prequel  can  get quite large.  They can be encoded in a
       compact binary form using pbsEncode, e.g.,

              pbsEncode anc.human-mouse.probs codefile > anc.human-mouse.bin

       although this encoding results in some loss of precision.  Encoded files  can  be  decoded
       using pbsDecode, e.g.,

              pbsDecode anc.human-mouse.bin codefile > anc.human-mouse.probs

       For  maximum  efficiency,  encode  ancestral reconstructions on the fly using the --encode
       option to prequel, e.g.,

              prequel --encode codefile mammals.fa mytree.mod anc

       Prequel can also be useful in optimizing a code based on training data.  The  --suff-stats
       option produces a more compact output file, which can then be fed to pbsTrain, e.g.,

              prequel  --suff-stats  mammals.fa  mytree.mod  training  pbsTrain  training.stats >


       --seqs, -s <seqlist>

       Only produce output for specified sequences.
              Argument should be comma-separated list of names of ancestral nodes.

       --exclude, -x (for use with --seqs) Exclude rather than include specified sequences.

       --keep-gaps, -k

       Retain gaps in output, as described above.

       --no-probs, -n

       Instead of reporting a probability distribution for each ancestral
              base, output the base with the maximum posterior probability.  Output  will  be  in
              FASTA  format  to  files  having  suffix  ".fa" rather than ".probs".  If used with
              --keep-gaps, gap characters ('-') will appear in reconstructed sequences.

       --suff-stats, -S

              Output a table of probability vectors and counts, pooling together all nodes of the
              tree  (or  a  subset defined by --seqs).  Produces a file that can be used for code
              estimation by pbsTrain.  Output file will have suffix ".stats".

       --encode, -e <code_file> Encode probabilities using given code and output as binary files.
              Output files will have suffix ".bin" rather than ".probs"

       --msa-format, -i FASTA|PHYLIP|MPM|MAF|SS

              Alignment  format  (default  is  to guess format from file content).  Note that the
              program msa_view can be used for conversion.

       --refseq, -r <fname>

              (for use with --msa-format MAF) Read the complete text of  the  reference  sequence
              from  <fname>  (FASTA  format)  and combine it with the contents of the MAF file to
              produce a  complete,  ordered  representation  of  the  alignment.   The  reference
              sequence of the MAF file is assumed to be the one that appears first in each block.

       --gibbs, -G <nsamples>

              (experimental)  Estimate  posterior  probabilities by Gibbs sampling rather than by
              the sum-product algorithm.  Sample each  sequence  <nsamples>  times  and  estimate
              posterior  probabilities  as fraction of times each base appeared at each position.
              This option is used by default if a dinucleotide or trinucleotide  model  is  given
              (exact inference not possible).   NOT YET IMPLEMENTED

       --help, -h

              Produce this help message.