Ubuntu Manpage: phyloFit - Fits one or more tree models to a multiple alignment of DNA

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example
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NAME

       phyloFit - Fits one or more tree models to a multiple alignment of DNA

DESCRIPTION

       Fits  one  or  more tree models to a multiple alignment of DNA sequences by maximum likelihood, using the
       specified tree topology and substitution model.  If categories of sites are defined  via  --features  and
       --catmap  (see  below), then a separate model will be estimated for each category.  A description of each
       model will be written to a separate file, with the suffix ".mod".  These .mod files minimally  include  a
       substitution  rate  matrix,  a  tree  with  branch  lengths,  and  estimates  of  nucleotide  equilibrium
       frequencies.  They may also include information about parameters for modeling rate variation.

SYNOPSIS

       phyloFit [OPTIONS] <msa_fname>

       <msa_fname> should be a multiple alignment in FASTA format or one of  several  alternative  formats  (see
       --msa-format).   For backward compatibility, this argument may be preceded by '-m' or '--msa'.  Note that
       --tree is required in most cases.  By default, all output files will  have  the  prefix  "phyloFit"  (see
       --out-root).

EXAMPLE

       (If you're like me, you want some basic examples first, and a list of all options later.)

       1. Compute the distance between two aligned sequences (in FASTA file pair.fa) under the REV model.

              phyloFit pair.fa

       (output  is  to  phyloFit.mod;  distance in substitutions per site appears in the TREE line in the output
       file)

       2. Fit a phylogenetic model to an alignment of human, chimp, mouse, and rat  sequences.   Use  the  HKY85
       substitution model.  Write output to files with prefix "myfile".

              phyloFit    --tree    "((human,chimp),(mouse,rat))"    --subst-mod    HKY85    --out-root   myfile
              primate-rodent.fa

       3. As above, but use the discrete-gamma model for rate variation, with 4 rate categories.

              phyloFit --tree "((human,chimp),(mouse,rat))"  --subst-mod  HKY85  --out-root  myfile  --nrates  4
              primate-rodent.fa

       4.  As  above,  but  use  genome-wide  data, stored in the compact "sufficient-statistics" format (can be
       produced with "msa_view -o SS").

              phyloFit --tree "((human,chimp),(mouse,rat))"  --subst-mod  HKY85  --out-root  myfile  --nrates  4
              --msa-format SS primate-rodent.ss

       5.  Fit  a context-dependent phylogenetic model (U2S) to an alignment of human, mouse, and rat sequences.
       Use an EM algorithm for parameter optimization and relax the convergence criteria a bit (recommended with
       context-dependent   models).    Write   a  log  file  for  the  optimization  procedure.   Consider  only
       non-overlapping pairs of sites.

              phyloFit --tree "(human,(mouse,rat))" --subst-mod U2S --EM --precision MED --non-overlapping --log
              u2s.log --out-root hmr-u2s hmr.fa

       6.  As above, but allow overlapping pairs of sites, and compute likelihoods by assuming Markov-dependence
       of columns (see Siepel & Haussler, 2004).  The EM algorithm can no longer be used (optimization  will  be
       much slower).

              phyloFit  --tree  "(human,(mouse,rat))"  --subst-mod  U2S  --precision  MED  --log  u2s-markov.log
              --markov hmr.fa

       7. Compute a likelihood using parameter estimates obtained in (5) and an assumption of Markov dependence.
       This provides a lower bound on the likelihood of the Markov-dependent model.

              phyloFit --init-model hmr-u2s.mod --lnl --markov hmr.fa

       8.  Given  an alignment of several mammalian sequences (mammals.fa), a tree topology (tree.nh), and a set
       of gene annotations in GFF (genes.gff), fit  separate  models  to  sites  in  1st,  2nd,  and  3rd  codon
       positions.  Use the REV substitution model.  Assume coding regions have feature type 'CDS'.

              phyloFit  --tree tree.nh --features genes.gff --out-root mammals-rev --catmap "NCATS = 3; CDS 1-3"
              --do-cats 1,2,3 mammals.fa

       (output will be to mammals-rev.cds-1.mod, mammals-rev.cds-2.mod, and mammals-rev.cds-3.mod)

OPTIONS

--tree, -t <tree_fname>|<tree_string>

(Required if more than three species, or more than two species and a non-reversible substitution
model, e.g., UNREST, U2, U3) Name of file or literal string defining tree topology. Tree must be
in Newick format, with the label at each leaf equal to the index or name of the corresponding
sequence in the alignment (indexing begins with 1). Examples: --tree "(1,(2,3))", --tree
"(human,(mouse,rat))". Currently, the topology must be rooted. When a reversible substitution
model is used, the root is ignored during the optimization procedure.

--subst-mod, -s JC69|F81|HKY85|HKY85+Gap|REV|SSREV|UNREST|R2|R2S|U2|U2S|R3|R3S|U3|U3S

(default REV).
Nucleotide substitution model. JC69, F81, HKY85

REV, and UNREST have the usual meanings (see, e.g., Yang, Goldman, and Friday, 1994). SSREV is a
strand-symmetric version of REV. HKY85+Gap is an adaptation of HKY that treats gaps as a fifth
character (courtesy of James Taylor). The others, all considered "context-dependent", are as
defined in Siepel and Haussler, 2004. The options --EM and --precision MED are recommended with
context-dependent models (see below).

--msa-format, -i FASTA|PHYLIP|MPM|MAF|SS (default is to guess format from file contents) Alignment
format. FASTA is as usual. PHYLIP is compatible with the formats used in the PHYLIP and PAML
packages. MPM is the format used by the MultiPipMaker aligner and some other of Webb Miller's
older tools. MAF ("Multiple Alignment Format") is used by MULTIZ/TBA and the UCSC Genome Browser.
SS is a simple format describing the sufficient statistics for phylogenetic inference (distinct
columns or tuple of columns and their counts). Note that the program "msa_view" can be used for
file conversion.

--out-root, -o <output_fname_root> (default "phyloFit"). Use specified string as root filename for all
files created.

--min-informative, -I <ninf_sites>

Require at least <ninf_sites> "informative" sites -- i.e., sites at which at least two non-gap and
non-missing-data ('N' or '*') characters are present. Default is 50.

--gaps-as-bases, -G Treat alignment gap characters ('-') like ordinary bases. By

default, they are treated as missing data.

--ignore-branches, -b <branches>

Ignore specified branches in likelihood computations and parameter estimation, and treat the
induced subtrees as independent. Can be useful for likelihood ratio tests. The argument
<branches> should be a comma-separated list of nodes in the tree, indicating the branches above
these nodes, e.g., human-chimp,cow-dog. (See tree_doctor --name-ancestors regarding names for
ancestral nodes.) This option does not currently work with --EM.

--quiet, -q Proceed quietly.

--help, -h

Print this help message. (Options for controlling and monitoring the optimization procedure)

--lnl, -L

(for use with --init-model) Simply evaluate the log likelihood of the specified tree model,
without performing any further optimization. Can be used with --post-probs, --expected-subs, and
--expected-total-subs.

--EM, -E

Fit model(s) using EM rather than the BFGS quasi-Newton algorithm (the default).

--precision, -p HIGH|MED|LOW

(default HIGH) Level of precision to use in estimating model parameters. Affects convergence
criteria for iterative algorithms: higher precision means more iterations and longer execution
time.

--log, -l <log_fname>

Write log to <log_fname> describing details of the optimization procedure.

--init-model, -M <mod_fname> Initialize with specified tree model. By choosing good

starting values for parameters, it is possible to reduce execution time dramatically. If this
option is chosen, --tree is not allowed. The substitution model used in the given model will be
used unless --subst-mod is also specified. Note: currently only one mod_fname may be specified;
it will be used for all categories.

--init-random, -r Initialize parameters randomly. Can be used multiple times to test

whether the m.l.e. is real.

--seed, -D <seed>

Provide a random number seed for choosing initial parameter values (usually with --init-random,
though random values are used in some other cases as well). Should be an integer >=1. If not
provided, seed is chosen based on current time.

--init-parsimony, -y Initialize branch lengths using parsimony counts for given data. Only currently
implemented for models with single character state (ie, not di- or tri-nucleotides). Other --init
options such as --init-random or --init-model can be used in conjunction to initialize
substitution matrix parameters.

--print-parsimony, -Y <filename>

Print parsimony score to given file, and quit.
(Does not optimize

or report likelihoods).

--clock, -z Assume a molecular clock in estimation. Causes the distances to all descendant leaves to be
equal for each ancestral node and cuts the number of free branch-length parameters roughly in
half.

--scale-only, -B

(for use with --init-model) Estimate only the scale of the tree, rather than individual branch
lengths (branch proportions fixed). Equilibrium frequencies and rate-matrix parameters will still
be estimated unless --no-freqs and --no-rates are used.

--scale-subtree, -S <node_name> (for use with --scale-only) Estimate separate scale factors for subtree
beneath identified node and rest of tree. The branch leading to the subtree is included with the
subtree. If ":loss" or ":gain" is appended to <node_name>, subtree scale is constrained to be
greater than or less than (respectively) scale for rest of tree.

--estimate-freqs, -F

Estimate equilibrium frequencies by maximum likelihood, rather than approximating them by the
relative frequencies in the data. If using the SSREV model, this option implies --sym-freqs.

--sym-freqs, -W

Estimate equilibrium frequencies, assuming freq(A)=freq(T) and freq(C)=freq(G). This only works
for an alphabet ACGT (and possibly gap). This option implies --estimate-freqs.

--no-freqs, -f

(for use with --init-model) Do not estimate equilibrium frequencies; just use the ones from the
given tree model.

--no-rates, -n

(for use with --init-model) Do not estimate rate-matrix parameters; just use the ones from the
given tree model.

--ancestor, -A <seqname> Treat specified sequence as the root of the tree. The tree topology must define
this sequence to be a child of the root (in practice, the branch from the root to the specified
sequence will be retained, but will be constrained to have length zero).

--error, -e <filename>

For each parameter, report estimate, variance, and 95%% confidence interval, printed to given
filename, one parameter per line.

--no-opt, -O <param_list> Hold parameters listed in comma-separated param_list constant at initial
values. This applies only to the "main" model, and not to any models defined with the --alt-mod
option. Param list can contain values such as "branches" to hold branch lengths constant,
"ratematrix", "backgd", or "ratevar" to hold entire rate matrix, equilibrium frequencies, or rate
variation parameters constant (respectively). There are also substitution model-specific
parameters such as "kappa" (transition/transversion rate ratio). Note: to hold certain branches
constant, but optimize others, put an exclamation point in the newick-formatted tree after the
branch lengths that should be held constant. This can be useful for enforcing a star-phylogeny.
However, note that the two branches coming from root of tree are treated as one. So they should
both be held constant, or not held constant. This option does *not* work with --scale-only or
--clock.

--bound <param_name[lower_bound,upper_bound]> Set boundaries for parameter. lower_bound or upper_bound
may be empty string to keep default. For example --bound gc_param[1,] will

set the lower bound for gc_param to 1 (keeping upper bound at infinity), for a GC model. Only
applies to parameters for model in the "main" tree, but similar syntax can be used within the
--alt-mod arguments. Can be used multiple times to set boundaries for different parameters.

--selection <selection_param>

Use selection in the model (is also implied if --init-model is used and contains selection
parameter). Selection scales rate matrix entries by selection_param/(1-exp(-selection-param));
this is done after rate matrix is scaled to set expected number of substitutions per unit time to
1. If using codon models selection acts only on nonysynonymous mutations. (Options for modeling
rate variation)

--nrates, -k <nratecats> (default 1). Number of rate categories to use. Specifying a

value of greater than one causes the discrete gamma model for rate variation to be used (Yang,
1994).

--alpha, -a <alpha> (for use with --nrates). Initial value for alpha, the shape parameter of the gamma
distribution. Default is 1.

--rate-constants, -K <rate_consts>

Use a non-parameteric mixture model for rates, instead of assuming a gamma distribution. The
argument <rate_consts> must be a comma-delimited list explicitly defining the rate constants to be
used. The "weight" (mixing proportion) associated with each rate constant will be estimated by EM
(this option implies --EM). If --alpha is used with this option, then the mixing proportions will
be initialized to reflect a gamma distribution with the specified shape parameter. (Options for
separate handling of sites in different annotation categories)

--features, -g <fname>

Annotations file (GFF or BED format) describing features on one or more sequences in the
alignment. Together with a category map (see --catmap), will be taken to define site categories,
and a separate model will be estimated for each category. If no category map is specified, a
category will be assumed for each type of feature, and they will be numbered in the order of
appearance of the features. Features are assumed to use the coordinate frame of the first
sequence in the alignment and should be non-overlapping (see 'refeature --unique').

--catmap, -c <fname>|<string>

(optionally use with --features) Mapping of feature types to category numbers. Can either give a
filename or an "inline" description of a simple category map, e.g., --catmap "NCATS = 3 ; CDS 1-3"
or --catmap "NCATS = 1 ; UTR 1". Note that category 0 is reserved for "background" (everything
that is not described by a defined feature type).

--do-cats, -C <cat_list>

(optionally use with --features) Estimate models for only the specified categories
(comma-delimited list categories, by name or numbera). Default is to fit a model for every
category.

--reverse-groups, -R <tag>

(optionally use with --features) Group features by <tag> (e.g., "transcript_id" or "exon_id") and
reverse complement segments of the alignment corresponding to groups on the reverse strand.
Groups must be non-overlapping (see refeature --unique). Useful with categories corresponding to
strand-specific phenomena (e.g., codon positions). (Options for context-dependent substitution
models)

--markov, -N

(for use with context-dependent substitutions models and not available with --EM.) Assume Markov
dependence of alignment columns, and compute the conditional probability of each column given its
N-1 predecessors using the two-pass algorithm described by Siepel and Haussler (2004). (Here, N
is the "order" of the model, as defined by --subst-mod; e.g., N=1 for REV, N=2 for U2S, N=3 for
U3S.) The alternative (the default) is simply to work with joint probabilities of tuples of
columns. (You can ensure that these tuples are non-overlapping with the --non-overlapping
option.) The use of joint probabilities during parameter estimation allows the use of the --EM
option and can be much faster; in addition, it appears to produce nearly equivalent estimates. If
desired, parameters can be estimated without --markov, and then the likelihood can be evaluated
using --lnl and --markov together. This gives a lower bound on the likelihood of the
Markov-dependent model.

--non-overlapping, -V (for use with context-dependent substitution models; not compatible with --markov,
--features, or --msa-format SS) Avoid using overlapping tuples of sites in parameter estimation.
If a dinucleotide model is selected, every other tuple will be considered, and if a nucleotide
triplet model is selected, every third tuple will be considered. This option cannot be used with
an alignment represented only by unordered sufficient statistics. (Option for lineage-specific
models)

--label-branches branch1,branch2,branch3...:label

Create a group of branches by giving a set of branches a single label. The label should be a word
which does not contain special characters (in particular, no spaces, brackets, parentheses, pound
signs, commas, or colons). The label is for use with --alt-model option below, so that an
alternate model can be defined for a set of branches. A branch is specified by the name of the
node which is a descendant of that branch.

For example, --label-branches hg18,chimp,hg18-chimp:HC will apply the label "HC" to the
hg18,chimp,and hg18-chimp branches in the following tree: (((hg18,chimp)hg18-chimp,
(mouse,rat)mouse-rat)

The same label could be defined without using --label-branches by specifying the tree (either on
the command-line or within init-model) as follows: (((hg18 # HC, chimp #HC)#HC, (mouse,rat))

--label-subtree node[+]:label Similar to label-branches, except labels the entire subtree of the named
node. If the node name is followed by a "+" sign, then includes the branch leading up to the node
in the subtree.

--alt-model, -d <label:(model|param_list)> Create a lineage-specific substitution model on a group of
branches. The group is defined by a label, which can be specified within the tree string (using
the # sign notation), or by using the --label-branches or --label-subtree arguments. If the
alt-model applies to only a single branch, labelling is not necessary and the name of the node
descending from the branch can be used instead. See --label-branches above for more details on
labelling groups of branches. If a name of a substitution model (HKY85, REV, UNREST, etc) is
given after the colon, then this model will be used for the group of branches, and parameters
relevant to the model will be estimated separately in this group. This model may be different (or
the same) as the model used in the rest of the tree, but it must have the same number of states
and be of the same order as the model used for the rest of the tree.

Alternately, a list of parameter names can be given after the colon. In this case, the same
substitution model will be used for the entire tree, but the parameters listed will be estimated
separately in the specified group of branches.

The parameter names are model-specific, and include "kappa" for HKY models, "alpha" for GC models,
"ratematrix" to specify all rate-matrix parameters in general models, and "backgd" for the
equilibrium background frequencies. The parameter names may optionally be followed by boundaries
in square brackets to specify parameter bounds, as described in --bound option.

The --alt-model argument may be used multiple times, if one wishes to (for example) optimize a
parameter independently on several different groups of branches. Example: phyloFit align.fa
--subst-mod HKY85 \ --tree "(human, (mouse#MR, rat#MR)#MR, cow)"\ --alt-model "MR:kappa[0, 1]"

will estimate the HKY85 parameter kappa separately on the mouse/rat subtree, and constrain kappa
between 0 and 1. The quotes are often necessary to prevent the square brakcets from being parsed
by the shell. The same model could be achieved with:

phyloFit align.fa --subst-mod HKY85 \ --tree "(human, (mouse,rat)mouse-rat, cow)"\
--label-branches mouse,rat,mouse-rat:MR \ --alt-model "MR:kappa[0,1]" or

phyloFit align.fa --subst-mod HKY85 \ --tree "(human, (mouse,rat)mouse-rat, cow)" \
--label-subtree "mouse-rat+:MR" \ --alt-model "MR:kappa[0,1]"

(Options for posterior probabilities)

--post-probs, -P

Output posterior probabilities of all bases at all ancestral nodes. Output will be to auxiliary
file(s) with suffix ".postprobs".

--expected-subs, -X

Output posterior expected number of substitutions on each branch at each site, summed across all
types of substitutions. Output will be to auxiliary file(s) with suffix ".expsub".

--expected-subs-col, -J

Output posterior expected number of substitutions of each type on each branch, for each site.
Output will be to auxiliary file(s) with suffix .expcolsub

--expected-total-subs, -Z

Output posterior expected number of substitutions of each type on each branch, summed across all
sites. Output will be to auxiliary file(s) with suffix ".exptotsub".

--column-probs, -U

(for use with -init-model; implies --lnl)
Output a separate log

probability for each type of column in the input.
Output will

be to a file with suffix ".colprobs".
Values are log base 2.

(Options for estimation in sliding window)

--windows, -w <size,shift> Apply a sliding window to the alignment, and fit a separate tree to each
window. Arguments specify size of window and amount by which to shift it on each iteration, both
in bases of the first sequence in the alignment (assumed to be the reference sequence). Separate
versions of all output files will be created for each window.

--windows-explicit, -v <window_coord_list> Like --windows, except that all start and end coordinates must
be explicitly specified. Each successive pair of numbers is interpreted as defining the start and
end of a window. Can be used with a two-column file and the '*' operator, e.g.,
--windows-explicit '*mycoords'.

NAME

DESCRIPTION

SYNOPSIS

EXAMPLE

OPTIONS

SEE ALSO