PAUP is run by a pre-created XML file in the CIPRES Portal:

The XML file is here:

<?xml version="1.0" encoding="UTF-8"?>
<command-object>

It delivers the command line

default hsearch swap=tbr multrees=no timelimit=None reconlimit=Infinity [paup.Wrap.n.ratchet.reps=200] [paup.Wrap.ratchet.prop=0.2] [paup.Wrap.ratchet.seed=0]

These commands are explained below. Please see the PAUP manual [pdf] for greater detail.

default hsearch swap=tbr multrees  timelimit=None reconlimit=Infinity

Syntax
HSEARCH [options] ; 

The HSEARCH command is used to search for optimal trees using heuristic algorithms. 

Available options

• *START = STEPWISE|NJ|CURRENT|tree-number [-tree-number ]
• ADDSEQ = SIMPLE|CLOSEST|ASIS|RANDOM|FURTHEST

• NREPS = integer-value
• RSEED = integer-value
• SAVEREPS = YES|NO
• RSTATUS = YES|NO
• REFTAX = integer-value
• HOLD = integer-value|NO
• SWAP = NONE|NNI|SPR|TBR
• MULTREES = YES|NO
• KEEP = real-value|NO
• NBEST = integer-value|NO
• ALLSWAP = YES|NO
• RECONLIMIT = integer-value|INFINITY
• ENFORCE = YES|NO
• CONSTRAINTS = constraint-name
• CONVERSE = YES|NO
• USENONMIN = YES|NO
• STEEPEST = YES|NO
• ABORTREP = YES|NO
• NCHUCK = integer-value
• CHUCKSCORE = real-value|NO

• *RETAIN = YES|NO
• • STATUS = YES|NO
• DSTATUS = integer-value|NONE
• RANDOMIZE = ADDSEQ|TREES
• TIMELIMIT = integer-value|NONE
• REARRLIMIT = integer-value|NONE
• LIMITPERREP = NO|YES

 

*Option is nonpersistent 

 Description of options

START = STEPWISE|NJ|CURRENT|tree-number [-tree-number]
 
When parsimony or likelihood is selected as the optimality criterion (see the "Set" command described on page 114) stepwise addition becomes the default procedure to obtain starting trees for branch swapping. Neighbor joining becomes the default procedure when distance is selected as the optimality criterion. Neighbor joining (START = NJ) may be used to obtain starting trees only if the optimality criterion is set to maximum likelihood or distance. Alternatively, you can request that all of the trees currently in memory (START = CURRENT) or a subset of the current trees (START = tree-number [-tree-number]) be used as a starting points for branch swapping.

ADDSEQ = SIMPLE|CLOSEST|ASIS|RANDOM|FURTHEST
 
Use ADDSEQ to specify the addition sequence to be used in the stepwise addition procedure. SIMPLE addition sequence is the default procedure used when parsimony is selected as the optimality criterion; ASIS is the default under the likelihood criterion.

Options for ADDSEQ = SIMPLE:

REFTAX = reference-taxon-number

By default, the first taxon in the data file is used as the reference taxon. Use REFTAX to specify an alternate reference taxon. This option is relevant only for unrooted-tree searches. For rooted-tree searches, the hypothetical ancestor (see "Ancstates" on page 36 and "Assume" on page 36) is used as the reference taxon.

Options for ADDSEQ = RANDOM:

NREPS = integer-value

Use NREPS to specify the number of random-addition-sequence replications to be performed. The default is 10.

RSEED = integer-value

By default, PAUP* references the system clock to initialize the seed used to generate pseudorandom numbers used to obtain random-addition-sequences (i.e., RSEED = 0). An explicit seed may be specified to override the system clock default. (See "INITSEEDS = 0|1" on page 116 for more details.)

SAVEREPS = YES|NO

If SAVEREPS = YES, then optimal trees from each repetition are saved even if they are not optimal over all repetitions.

RANDOMIZE = ADDSEQ|TREES

If RANDOMIZE = TREES, initial trees are random trees rather than trees found by random-addition-sequence.

RSTATUS = YES|NO

If you specify RSTATUS = YES, a status report showing the results of each random-addition-sequence replication is output. The status report can be useful in evaluating the effectiveness of the heuristic search while the search is proceeding. 

Example 1

The following example shows the syntax used to execute a heuristic search with 20 random-addition-sequence replicates. A random number seed of 123 is used to generate random-addition-sequences.

hsearch addseq=random nreps=20 rseed=123;

HOLD = integer-value|NO

Specifies the number of trees to be held at each cycle of the stepwiseaddition procedure. By default, HOLD = 1, so that a single tree is held at each step. While setting n > 1 sometimes improves the score of the tree found by stepwise addition it will aslo increase the time required to complete the addition of sequences.

SWAP = TBR|SPR|NNI|NONE

Specifies the algorithm used by branch-swapping: TBR = tree bisection-reconnection, SPR = subtree pruning-regrafting, NNI = nearest-neighbor interchange, NONE = No branch swapping performed. NNI rearrangements are a subset of those done by SPR, and SPR rearrangements are a subset of those done by TBR. Ordinarily, you will use TBR, but SPR or NNI can be used to reduce search times.

MULTREES = YES|NO

Ordinarily, PAUP* saves all minimal trees it finds during branch swapping. You can override the default with MULTREES=NO to save only one of the best trees found. Use of MULTREES = NO is not recommended, as it can drastically reduce the ability of branch swapping to find the best tree. (This option is synonymous with MULPARS option in earlier versions of PAUP.)

NBEST = integer-value|NO

Use NBEST to save the N best trees discovered during the search according to the optimality criterion in effect. The NBest option cannot be used when random-addition-sequence is in effect (i.e., ADDSEQ = RANDOM).

ALLSWAP = YES|NO

Unless ALLSWAP = YES is specified, the trees saved by setting NBest > 1 will include only those trees encountered during a search for optimal trees; no special effort is made to find additional trees that might be still better. If ALLSWAP = YES is requested, then all trees saved are themselves input to the branch swapping procedure, making it much more likely that the optimal NBEST trees will be found. Setting ALLSWAP = YES can dramatically increase the search time, however.

RECONLIMIT = integer-value|INFINITY

The reconnection limit option limits the scope of SPR and TBR rearrangements. If an integer-value is specified, the value corresponds to the sum of the number of nodes between each reconnected branch and the nodes incident to the branch that was cut for pruning (SPR) or bisection (TBR). A rearrangement limit of 1 corresponds to nearest-neighbor interchanges. The default limit is set to infinity.

USENONMIN = YES|NO

It is possible that the trees in memory at the time branch-swapping begins are not all equal in score. By default, only the best available trees are input to the branch-swapping procedure. If you want to swap on nonminimal trees as well, specify USENONMIN=YES.

STEEPEST = YES|NO

Specify STEEPEST to request use of the steepest-descent modification in the branch-swapping procedure. STEEPEST = NO reverses the effect of a previous STEEPEST specification.

NCHUCK = integer-value
CHUCKSCORE = real-value|NO
If this pair of options is used, no more than the number of trees specified by the NCHUCK option of score greater than or equal to the score specified by the CHUCKSCORE option will be retained in a search (or in a random-addition-sequence replicate). These options allow a user to effectively set a maxtrees limit (see page 119) when swapping on less "promising" trees and remove the limit for more "promising" trees. 

Example 2

In the following example of the HSEARCH command the NCHUCK and CHUCKSCORE options are used to save a maximum of 100 trees with scores of 600 or above; no limit is imposed for trees less than 600.
hsearch nchuck=100 chuckscore=600;

ABORTREP = YES|NO

If ABORTREP is requested and NCHUCK and CHUCKLEN values have been specified, the current random-addition-sequence replicate will be aborted if the "chucking" limits are hit.
RETAIN = number-of-trees-to-retain

The first number-of-trees-to-retain will be retained in memory throughout the search. (Ordinarily, all trees initially in memory will be replaced by trees found during the search.) The RETAIN option is not persistent; you must reset it for every HSEARCH command if you want to continue retaining the same set of initial trees.

TIMELIMIT = integer-value|NONE

If an integer-value is specified, the search will be limited to a userspecified length of time, where the integer-value is the number of seconds to search.

REARRLIMIT = integer-value|NONE

If an integer-value is specified, the search will be limited to a userspecified number of tree rearrangements (branch swaps), where the integer-value is the maximum number of rearrangements to be performed.

LIMITPERREP = NO|YES

By default, the TIMELIMIT and REARRLIMIT options apply to the entire search in random-addition-sequence searches. However, if you request LIMITPERREP=YES, then the limits are imposed separately for each addition-sequence replicate. For replicated searches such as the bootstrap (page 39), the jackknife (page 77), and the partition-homogeneity test (page 70) the limits are always applied separately for each search.

Example 3
The following example of the HSEARCH command imposes a rearrangement limit of 5000 for each of 20 random-addition-sequence replicates.
hsearch addseq=random nreps=20 rearrlimit=5000

limitperrep=yes;

See "Options And Subcommands Affecting Multiple Commands" on page 30 for a description of the following options:
KEEP = keep-score
ENFORCE = YES|NO
CONSTRAINTS = constraint-name
CONVERSE = YES|NO
STATUS = YES|NO
DSTATUS = integer-value|NONE

 

CIPRES is a Collaboration of the Following Institutions:
American Museum of Natural History, Florida State University, New Jersey Institute of Technology, North Carolina State University, Rice University, San Diego Supercomputer Center, Texas A&M, University of Arizona, University of British Columbia, University of California at Berkeley, University of California at San Diego, University of Connecticut, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University. xhtml | css