PSODA Manual

The following commands are available in Psoda. They can either be entered into a PAUP or PSODA block in a nexus file, or entered in the "commands" dropdown in the PSODA gui window. Examples are given for many of the commands along with a description of the parameters.

• decrement

    Description: Decrement Instruction

    Usage: *decrement (*name = "");
    Parameters: 
        *name   :   No Description Provided

Example:
• empty

    Description: Execute a psoda command
    Usage: *empty ();
    Parameters: 

• increment

    Description: Increment a value.
    Usage: *increment (*name = "");
    Parameters: 
        *name   :   No Description Provided

• update

    Description: Change the value of a variable.
    Usage: *update (*name = "", *value = "");
    Parameters: 
        *name   :   The variable name that will be given a value
        *value  :   The value that should be assigned to the variable

• var

    Description: Declare a variable

    Usage: *var (*name = "", *value = "");
    Parameters: 
        *name   :   No Description Provided
        *value  :   No Description Provided

• align

    Description: Take an unaligned dataset with taxa of potentially different lengths and create an aligned dataset with gaps inserted to create a rectangular matrix.
    Usage: align (classic = "No", endgap = "yes", gapdist = 4, gapext = "", gapopen = "", guidetree = "", name = "", outfile = "", output = "fasta", prog = "pmsa", submat = "");
    Parameters: 
        classic :   if Yes, use the stock (unoptimized) progressivive sequence alignment methods of iterating through every character in one sub-alignment with every other character in the other alignment.  If No, use the optimizied MultChars.
        endgap  :   Penalize Leading Gaps
        gapdist :   penalize opening a new gap within this distance to another gap
        gapext  :   Gap Extension defaults to -0.2 for Protein sequences and -6.6 for everything else
        gapopen :   Gap Open Penalty defaults to -10 for protein sequences and -15 for everything else
        guidetree   :   Create a UPGMA guide tree if NULL
        name    :   If name is non-empty, the resulting aligned dataset will be added to the interpreter's dataset map with this name.  If this command is used as a function a reference to the stored dataset will be returned and if no name was given, a unique identifier will be assigned
        outfile :   File name to save the output to
        output  :   The output format
        prog    :   Program used for alignment.  Progressive Multiple Sequence Alignment is currently the only option
        submat  :   substition matrix to use for alignment.  Possible values include: IUB, BLOSUM62, SCHNEIDER, LuthyA, LuthyB, LuthyL, identity, or a filename with the matrix.

• BackupRepository

    Description: Make a copy of the tree repository into the accumulator.
    Usage: BackupRepository ();
    Parameters: 

• bandb

    Description: Branch and Bound Command (Not Yet Implemented).
    Usage: bandb ();
    Parameters: 

• BayesSearch

    Description: Use mrbayes to perform a search.  This calls an external program to perform the search and then inserts the resulting tree into the repository.
    Usage: BayesSearch (bayesargs = "lset nst=6 rates=invgamma;\n", iterations = "0");
    Parameters: 
        bayesargs   :   The parameters passed to mrbayes.  See the documentation for Mrbayes for details
        iterations  :   The number of iterations.  If zero, then continue until the average standard deviation of split frequencies is less than 0.1

• bibliography

    Description: Print out a bibliography of references for programs included in PSODA.
    Usage: bibliography ();
    Parameters: 

• bootstrap

    Description: Perform Bootstrap. Randomly reweight columns of the alignment matrix and calculate the optimal tree based on that reweighting.  Then generate a consensus based on all of the trees generated by reweightings
    Usage: bootstrap (blocksize = 10, bseed = "clock", conlevel = 50, keepall = "no", nchar = "current", nreps = 100, search = "heuristic", wts = "simple");
    Parameters: 
        blocksize   :   Bootstrap block size for dependent columns
        bseed   :   Random number generator seed. Default is seed from clock
        conlevel    :   Confidence Level for boostrap consensus
        keepall :   Keep all trees? (Not currently implemented)
        nchar   :   The number of characters to reweight.  A value of current reweights all columns
        nreps   :   Number of replicates (Number of times to reweight).
        search  :   Search Strategy to use.  Heuristic uses TBR, nj=Neighbor Joining, upgma=Unweighted Pair Group Method using Arithmetic Averages
        wts :   Not currently implemented

• break

    Description: Break out of a Switch statement.
    Usage: break ();
    Parameters: 

• checkParsimony

    Description: Parsimony validation test.
    Usage: checkParsimony (construct = "sampling", cpseed = "time", criterion = "parsimony", iterations = 2147483647, lbshorten_method = "substitution", longesttaxa = "_calculate_", maxtrees = 2147483647, nreps = 1, start = "stepwise", sub_frequency = "0.75", swap = "TBR", wantrecursion = "FALSE");
    Parameters: 
        construct   :   Use ancestor state constructed by sampling or parsimony
        cpSeed  :   Random seed can be specified, otherwise, use the current time
        criterion   :   Optimality criteria
        iterations  :   Number of iterations to perform
        lbshorten_method    :   Method to shorten long branch
        longestTaxa :   Unless specified by the user, the longest taxa will be calculated using parsimony criteria.
        maxTrees    :   Maximum number of trees to keep in the repository
        nreps   :   Number of Replicates
        start   :   Start Tree generation method
        sub_frequency   :   Substitution Frequency
        swap    :   Swapping method
        wantRecursion   :   Recursion (Not currently Implemented)

• CombineRepositories

    Description: If the accumulator is better than the repository, replace the repository with the accumulator
    Usage: CombineRepositories ();
    Parameters: 

• ConstructAncestorStates

    Description: Construct the ancestral character states for a tree

    Usage: ConstructAncestorStates (assign = "yes", display = "yes");
    Parameters: 
        assign  :   assign the computed ancestral states to ancester data structures
        display :   display states

• contree

    Description: Compute the Consensus tree
    Usage: contree (grpfreq = "false", indices = "false", majrule = "false", percent = 100, replace = "false", showtree = "true", strict = "true", usetreewts = "false");
    Parameters: 
        grpfreq :   No Description Provided
        indices :   No Description Provided
        majrule :   No Description Provided
        percent :   No Description Provided
        replace :   No Description Provided
        showtree    :   No Description Provided
        strict  :   No Description Provided
        usetreewts  :   No Description Provided

• DeleteData

    Description: Deletes a dataset from the interpreter's dataset map.
    Usage: DeleteData (name = "*default");
    Parameters: 
        name    :   The name of the dataset to delete

• DeleteTree

    Description: Deletes a tree from the interpreter's tree map.
    Usage: DeleteTree (name = "*default");
    Parameters: 
        name    :   The name of the tree to delete

• display

    Description: Display a visualization of the tree space

    Usage: display (style = "MDS", terminal = "gnuplot");
    Parameters: 
        style   :   Which display style should be used
        terminal    :   How should the visualization be displayed

• dset

    Description: Execute a psoda command
    Usage: dset ();
    Parameters: 

• execute

    Description: Execute an external program

    Usage: execute (command = "");
    Parameters: 
        command :   No Description Provided

• export

    Description: Export the dataset with different formats

    Usage: export (file = "", format = "fasta");
    Parameters: 
        file    :   No Description Provided
        format  :   No Description Provided

• getBestScore

    Description: Get the score of the best tree in the Tree Repository
    Usage: getBestScore (eliminate = "True");
    Parameters: 
        eliminate   :   If true, all but the best tree are eliminated from the tree repository

• getNumChars

    Description: Get the number of characters in the alignment
    Usage: getNumChars ();
    Parameters: 

• gettrees

    Description: Get trees from a file and put them in the tree repository
    Usage: gettrees (file = "");
    Parameters: 
        file    :   The file from which the trees should be read

• getWeightsLength

    Description: Get the Length of the weights vector.  This should be the same as the number of characters in the alignment.
    Usage: getWeightsLength ();
    Parameters: 

• GradientDescent

    Description: Perform a gradient descent search for trees.
    Usage: GradientDescent (continue = 10, start = "stepwise");
    Parameters: 
        continue    :   How many times should the search continue to look after no improvement
        start   :   Where should the starting trees for the Gradient Descent Search come from

• graph

    Description: Enable the graph in the GUI.
    Usage: graph (start = "no", stop = "no");
    Parameters: 
        start   :   No Description Provided
        stop    :   No Description Provided

• help

    Description: Prints usage information about a given command (note: the usage for this command differs from the typical name=value paradigm)
The help command displays the usage for PsodaScript commands whether BuiltIn or UserDefined.


Examples:
  help "print"; [ displays the help information for the 'print' command]
  help;         [ displays the help information for the 'help' command]

    Usage: help *name;
    Parameters: 
        *name   :   the name (as a string) of the command for which to print the usage information

• hsearch

    Description: Heuristic Search for Phylogenetic Trees with optimal score.
    Usage: hsearch (aligned = "FALSE", criterion = "parsimony", iterations = 2147483647, maxtrees = 1000, nreps = 1, start = "stepwise", swap = "TBR", wantrecursion = "FALSE");
    Parameters: 
        aligned :   If this value is TRUE, then run the search even if the dataset is not aligned.  If the dataset is aligned, this parameter will not make a difference.
        criterion   :   Criterion can be "likelihood" or "parsimony"
        iterations  :   The number of iterations to search through.  Each iteration takes one split point in the tree and computes all possible rearrangements of the subtrees.
        maxTrees    :   The maximum number of trees with the best score to keep in the repository.  This may be limited by the amount of memory on your machine or in the Java Virtual Machine
        nreps   :   Number of replicate trees created in stepwise tree creation
        start   :   Where should the starting tree for the HSearch come from: stepwise, nj=neighbor joining, upgma, current
        swap    :   What method should be used for swaping.  Possible values are TBR, sectarian(computes a window over the tree that is 5 brances long and computes the best resolution for those branches, holding everything else constant), resolve (computes a consensus tree, then uses TBR to create a bifurcating tree for all unresolved nodes), none
        wantRecursion   :   Turn Recursive TBR on.  Find a tree using the most optimal subtrees

• interactive

    Description: Execute an interactive instruction.
    Usage: interactive (code = "", echocode = 1);
    Parameters: 
        code    :   The code that you pass in via this parameter will be executed by a PSODA interpreter
        echoCode    :   If true, the code entered throught the 'code' parameter will be echoed to the console

• lbstest

    Description: Long Branch Shortening.
    Usage: lbstest (alltrees = "false", construct = "sampling", cpseed = "time", criterion = "parsimony", iterations = 2147483647, lbshorten_method = "substitution", longesttaxa = "_calculate_", maxtrees = 2147483647, nreps = 1, start = "stepwise", sub_frequency = "0.25", swap = "TBR", wantrecursion = "FALSE");
    Parameters: 
        alltrees    :   No Description Provided
        construct   :   No Description Provided
        cpSeed  :   No Description Provided
        criterion   :   No Description Provided
        iterations  :   No Description Provided
        lbshorten_method    :   No Description Provided
        longestTaxa :   No Description Provided
        maxTrees    :   No Description Provided
        nreps   :   No Description Provided
        start   :   No Description Provided
        sub_frequency   :   No Description Provided
        swap    :   No Description Provided
        wantRecursion   :   No Description Provided

• Limits

    Description: Set limits for variables.
    Usage: Limits (bound = "max", type = "int");
    Parameters: 
        bound   :   Which bound is being requested (either 'max' or 'min')
        type    :   Which data type is begin described (either 'int' or 'double')

• LoadData

    Description: Loads a dataset from a file.  Note that only the first datablock from the file will be kept.
    Usage: LoadData (file = "", makecurrent = "yes", name = "");
    Parameters: 
        file    :   The file from which the data should be read
        makeCurrent :   If 'yes', the loaded dataset will become the current dataset in the interpreter
        name    :   The dataset will be stored in the interpreter's map with the given name if name is not empty

• log

    Description: Execute a psoda command
    Usage: log ();
    Parameters: 

• lscores

    Description: Generate Likelihood scores for trees in the repository.
    Usage: lscores (file = "");
    Parameters: 
        file    :   File to save the likelihood scores to

• lset

    Description: Execute a psoda command
    Usage: lset ();
    Parameters: 

• MRP

    Description: Add a matrix representation for every tree in the repository.
    Usage: MRP (criterion = "parsimony", iterations = 2147483647, maxtrees = 1000, nreps = 1, start = "stepwise", swap = "TBR", wantrecursion = "FALSE");
    Parameters: 
        criterion   :   No Description Provided
        iterations  :   No Description Provided
        maxTrees    :   No Description Provided
        nreps   :   No Description Provided
        start   :   Where should the starting tree for the HSearch come from
        swap    :   What method should be used for swaping
        wantRecursion   :   No Description Provided

• neighborTest

    Description: Test neighbor joining
    Usage: neighborTest (alltrees = "false");
    Parameters: 
        alltrees    :   No Description Provided

• nj

    Description: Create a neighbor joining tree for the dataset.
    Usage: nj ();
    Parameters: 

• PercentIdentity

    Description: Calculate the percent identity for the alignment
    Usage: PercentIdentity (counts = "", endgap = "yes", gapext = "", gapopen = "", submat = "");
    Parameters: 
        counts  :   print matrix of accumulative pairwise (mis)matches
        endgap  :   penalize Leading Gaps?
        gapext  :   Gap Extension penalty
        gapopen :   Gap Open penalty
        submat  :   No Description Provided

• print

    Description: Evaluates the given expression and prints the string value to the console (note: the usage for this command differs from the typical name=value paradigm
    Usage: print *text;
    Parameters: 
        *text   :   any valid PSODA expression

• printmatrix

    Description: Save the matrix to a file.
    Usage: printmatrix (file = "psoda.matrix.out");
    Parameters: 
        file    :   File to save the matrix to

• pscores

    Description: Generate a parsimony score for every tree in the repository.
    Usage: pscores (file = "");
    Parameters: 
        file    :   File to save the parsimony scores to

• quit

    Description: Quit out of the interpreter.
    Usage: quit ();
    Parameters: 

• random

    Description: Generate a random number.
    Usage: random (max = 2147483647);
    Parameters: 
        max :   The maximum value for the random number

• randomMorph

    Description: Randomly split every tree in the repository and join it in a random spot
    Usage: randomMorph ();
    Parameters: 

• RAxMLSearch

    Description: Execute a raxml search.
    Usage: RAxMLSearch (raxargs = "-m GTRGAMMA");
    Parameters: 
        raxargs :   These are raxml parameters.  See the raxml manual for details.

• ResolveTrees

    Description: Given an unresolved tree, resolve it in all possible ways and put the trees in the repository.
    Usage: ResolveTrees ();
    Parameters: 

• return

    Description: Return from a function
    Usage: return (*value = "");
    Parameters: 
        *value  :   No Description Provided

• rsearch

    Description: Recursive search (Not currently implemented)
    Usage: rsearch ();
    Parameters: 

• savetrees

    Description: Save the trees in the repository to a file.
    Usage: savetrees (file = "psoda.out.tre");
    Parameters: 
        file    :   No Description Provided

• set

    Description: Set global parameters for instructions
    Usage: set (*command = "*all", *name = "", *value = "");
    Parameters: 
        *command    :   The default value for the given parameter will be set on this command (by default, the set is done on all commands that have the given parameter)
        *name   :   The name of the default parameter to be set
        *value  :   The value to which the parameter should be set

• showtrees

    Description: Print out the trees in the repository
    Usage: showtrees ();
    Parameters: 

• Source

    Description: Parses the PSODA program souce from the given file.  User-defined commands will be added to the running program while PSODA commands will be parsed and executed.
    Usage: Source (file = "");
    Parameters: 
        file    :   The file from which the program should be read

• srandom

    Description: Seed the random number generator.
    Usage: srandom (seed = "clock");
    Parameters: 
        seed    :   No Description Provided

• ssalign

    Description: Take an unaligned dataset with taxa of potentially different lengths and create an aligned dataset with gaps inserted to create a rectangular matrix.  Use the secondary structure to align the sequences using chemical properties with weights optimized for the particular secondary structure
    Usage: ssalign (classic = "No", endgap = "yes", gapdist = 4, gapext = "", gapopen = "", guidetree = "", outfile = "ssalignment.afa", outfilecombined = "", outfiless = "alignment.ss.afa", outputcombined = "", outputss = "fasta", prog = "default", submata = "", submatb = "", submatl = "");
    Parameters: 
        classic :   if Yes, use the stock (unoptimized) progressivive sequence alignment methods of iterating through every character in one sub-alignment with every other character in the other alignment.  If No, use the optimizied MultChars.
        endgap  :   Penalize Leading Gaps
        gapdist :   penalize opening a new gap within this distance to another gap
        gapext  :   Gap Extension defaults to -0.2 for Protein sequences and -6.6 for everything else
        gapopen :   Gap Open Penalty defaults to -10 for protein sequences and -15 for everything else
        guidetree   :   Create a UPGMA guide tree if NULL
        outfile :   File name to save the output to
        outfileCombined :   File name to save the combined output to
        outfileSS   :   File name to save the SS to
        outputCombined  :   The output format
        outputSS    :   The output format
        prog    :   Program used for alignment.  Progressive Multiple Sequence Alignment is currently the only option
        submata :   substition matrix to use for alignment in alpha helix regions.  Possible values include: IUB, BLOSUM62, SCHNEIDER, LuthyA, LuthyB, LuthyL, identity, or a filename with the matrix.
        submatb :   substition matrix to use for alignment in beta sheet regions.  Possible values include: IUB, BLOSUM62, SCHNEIDER, LuthyA, LuthyB, LuthyL, identity, or a filename with the matrix.
        submatl :   substition matrix to use for alignment in loop regions.  Possible values include: IUB, BLOSUM62, SCHNEIDER, LuthyA, LuthyB, LuthyL, identity, or a filename with the matrix.

• sspredict

    Description: Predict the secondary structure for a sequence using a neural network.
    Usage: sspredict ();
    Parameters: 

• StackTrace

    Description: Prints the stack trace to the console
    Usage: StackTrace ();
    Parameters: 

• StoreTree

    Description: Takes a tree from the current tree repository and stores a copy of it in the interpreter's tree map.
    Usage: StoreTree (name = "*default");
    Parameters: 
        name    :   The name by which the stored tree will be identified in the tree map

• StringLength

    Description: Calculate the string length of a variable
    Usage: StringLength (string = "");
    Parameters: 
        string  :   The string to be tested for length

• SubString

    Description: Find a substring
    Usage: SubString (first = 0, length = "", string = "");
    Parameters: 
        first   :   The index of the first character to take
        length  :   The resulting substring will be no longer than this length, but it may be shorter if the end of the input string is reached.  Passing an empty string as this parameter will result in going to the end of the string.
        string  :   The string to take from

• sumOfPairs

    Description: Calculate the sum of pairs metric for the alignment.
    Usage: sumOfPairs (endgap = "yes", gapext = "", gapopen = "", guidetree = "", outfile = "ssalignment.afa", output = "fasta", prog = "default", submata = "", submatb = "", submatl = "");
    Parameters: 
        endgap  :   No Description Provided
        gapext  :   No Description Provided
        gapopen :   No Description Provided
        guidetree   :   No Description Provided
        outfile :   No Description Provided
        output  :   No Description Provided
        prog    :   No Description Provided
        submata :   No Description Provided
        submatb :   No Description Provided
        submatl :   No Description Provided

• time

    Description: Get the current time.
    Usage: time ();
    Parameters: 

• treedist
• treeinfo

    Description: Execute a psoda command
    Usage: treeinfo ();
    Parameters: 

• upgma

    Description: Generate a UPGMA tree.
    Usage: upgma ();
    Parameters: 

• UseData

    Description: Uses a dataset from the interpreter's dataset map.
    Usage: UseData (name = "");
    Parameters: 
        name    :   The name of the dataset to use

• UseTree

    Description: Uses a tree from the interpreter's tree map by adding a copy of it to the current tree repository
    Usage: UseTree (clearrep = "yes", name = "*default");
    Parameters: 
        clearrep    :   If this parameter is 'yes', clears the contents of the tree repository before adding the tree
        name    :   The name of the tree to use

• weights

    Description: Adjust the weights across the columns of the alignment.
    Usage: weights ();
    Parameters: 

• weights reset

    Description: Reset the weights to the original values.
    Usage: weights reset ();
    Parameters: