Provided by: phast_1.4+dfsg-1_amd64 
NAME
prequel - Compute marginal probability distributions for bases at ancestral
DESCRIPTION
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 sites.
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).
EXAMPLE
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.,
TREE:
((human:0.101627,chimp:0.149870)primate:0.035401,(mouse:0.280291,rat:0.157212)rodent:0.035401)mammal;
then output will be to files named "anc.primate.probs", "anc.rodent.probs", and "anc.mammal.probs". (See
http://evolution.genetics.washington.edu/phylip/newicktree.html) If instead the ancestral nodes are
unlabeled, e.g.,
TREE: ((human:0.101627,chimp:0.149870):0.035401,(mouse:0.280291,rat:0.157212):0.035401);
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 example,
#p(A)
p(C) p(G) p(T)
0.001449
0.000039 0.998460 0.000052
0.998150
0.000065 0.001755 0.000030
0.000427
0.271307 0.000599 0.727668
0.001449
0.000039 0.998460 0.000052
0.025826
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(A)
p(C) p(G) p(T)
0.998150
0.000065 0.001755 0.000030
0.001449
0.000039 0.998460 0.000052
0.125811
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 > mammals.code
OPTIONS
--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.
prequel 1.4 May 2016 PREQUEL(1)