Optionally, the trees produced can be fused every certain number of rounds. This is a sort of ratchet, where the perturbation is provided, not by character reweighting, but instead by choosing subsets of taxa.
The sectors chosen are large, exclusive sectors size chosen so that it is below or above two sectors for the sector size to be ; this size can be changed, with "chunksize" --see syntax below ; the actual selections depend on the current random seed. Then, the down-pass states or observed states, if a terminal of the ith element in the list of descendants is chosen to represent the HTU states.
N is the tree from which pfijo is to be started if no N is specified, each of the trees in memory is sequentially subjected to pinon fijo. N steps with the user-defined weighting function. It checks by reference to specific groups i.
General syntax is defaults in square brackets : prunmaj T N1 N2 N Set only, don't run. The values are presented with an arbitrary rescaling between 0 and 1, with taxa having higher scores expected recall this is a heuristic! Checks whether additinal groups appear. Agreement subtrees maximize number of shared taxa, not number of shared groups although both are the same for binary input trees!
Saves or lists a single tree. If symbol "! PTNT manage runs in parallel parallel versions only. Keep in mind that versions for taxa or less can't communicate with versions for more than taxa mixing bit and bit versions should be ok. With this, it is possible to save communication time. If "swap N" is specified, then it swaps tree N deleting any preexisting trees in the task ; if several trees are to be swapped in parallel, it is best to use "again" instead of "begin" for each one, since "again" doesn't require that the data be re-sent to the task s "begin" does!
Using " Up to 32 jobs can be running at the same time; every job can have up to tasks. When no list of hosts is given, if the executing process is the master, all hosts but the current one are used, or, if the process is a slave, all hosts but the one where parent process runs. If neither numtasks nor hostlist are given, one task per available slave host is used except for exclusive sectors, which spawns as many tasks as selections. If you wish to specify the number of tasks to be spawned in a host or group of hosts , include the number of tasks in parenthesis right after the name of the host or group of hosts, i.
Current or reduced data are automatically passed to each of the daughter processes each of which has a different random seed. If a list of sectors follows N within square brackets , then only those sectors are effectively launched. This can be used to re-insert the resolution for the sector into the main tree, or combining the results for successive sector analyses, using the "freqdifs" command i.
Note: under "sec:chkroot" the number of sectors created by this options is determined at run-time; use the "treeparts" expression to find in advance how many. To create the HTU-s, the tree is dichotomized if needed. When done, task 0 has the final tree which, if no errors occur, is TBR-optimal.
If some error occurs e. This works best when trees are closest to optimal i. When using "swap", instructions to slave tasks are ignored tasks only swap tree, and return. If several "trees" selections are indicated, selection i is guaranteed to have at least Ni trees taken out of each set Si; up to 8 tree selections per job can be indicated. If the sets for each selection i are disjoint, total number of trees sent to each slave will be the summation of the individual Ni's; otherwise, it may be less.
A slave may begin other parallel jobs; if it does so, giving " User variables are interpreted on local host when using single quotes '0' and on slave host when using double quotes "0". It may be necessary if "goto" or "again" are to be applied to a job that had finished running, and the job is to be "waited" again.
Must be set in slave processes too. The default is using the current status, but this may create problems if a homogeneous cluster becomes heterogeneous or viceversa in the middle of a run.
Job s must have finished running or have been stopped with "ptnt stop job;". If jobs have not finished, "get" waits for the last one to finish or untill timed-out.
Alternatively, if using "! If a single job is being retrieved, maxtrees is reset automatically if needed ; if several jobs are retrieved at the same time, maxtrees is not reset excess trees are lost. If memory is reassigned e. Memory requirements on TNT are eased if this is done often. After setting disk data, subsequently started jobs can read the data from disk instead of having PVM transfer the data which is time and memory consuming , using the "dskdata" option.
The slave cannot find a tag within a loop, and must still be executing instructions skipto is ignored if slave is already on "return" stage, i. If a single job is being specified, a list of tasks s can be specified as well after a forward slash.
Note: this only gets the trees from immediate slaves not their children or grandchildren. Maxtrees reset automatically as in get , only when a single job is being spied. Optionally, stopping signal can be determined inside square brackets: wait, loops, search, or all.
Wait stops the monitoring for slaves present and future , but not calculations or searches themselves. Loops lets presently executed loops to continue, but subsequent ones are stopped.
Search assumes the timeout for present and subsequent searches to be always met; it doesn't stop other calculations such as consensus calculations.
All stops calculations, searches, monitoring wait , and loops. The default stopping signal which is the one get! This is also a plain command. TNT may freeze if a slave host died. If no condition is specified it waits for all tasks to finish. Options are: replications N, select N, strictperc N, majorcut N. Search commands given in square brackets. Option "allow" works as in the resample command. Options are: iter N number of iterations [no]equal periodic rounds with original weights [not] numsubs N number of replacements i.
The command calculates the edit cost Needleman-Wunsch of the sequences as they are A , and with one of the sequences reverse-complemented R. This command is useful for very poorly structured data sets e.
The number of nodes deleted can be a fixed proportion "pclip" or an absolute number "clip" , of terminals or clades of a specified "size". This is done repeatedly as in the ratchet ; optionally, it is possible to use the best results of the cycles as input for tree-hybridization with settings from "tfuse" command. One of the best trees produced by hybridization is then used to continue the rebuilding.
Options possibly preceded by "no" : clip J-K at every cycle, clip a number of nodes between J and K. If this not specified or 0 , then it uses "pclip". If this set to 0, then it uses "psize". Each round of hybridization will use the results from as many cycles as specified with "cycles". With "no", hybridization becomes easily stalled by using a fixed set of near-optimal trees. With "rebuild:;" current settings are displayed. The tags for groups which become paraphyletic are assigned to the now monophyletic complement group i.
Usage: "resample options [ search commands ];" Options are: jak use normal jacknifing i. This option should be used sparingly and only when you really know what you're doing! See below for details. This counts the proportion of groups out of the total supported groups in the reduced data set that are not supported in the complete data set wrong groups and the proportion of groups out of the total in reference tree N presu- mably, consensus of optimal trees for the complete data set that are not supported by the reduced data set mist groups.
All options are persistent, except taxon exclusion and "from" The backwards jacknife is not a measure of support, but provides instead a sort of stability test. The existing trees must be provided by the user, and should correspond to a set of optimal trees under current settings. Other than search commands, only the number of replications can be changed, and taxa can be disregarded.
This cannot be done when there are constraints or asymmetric Sankoff characters randomization is skipped. This may save time in very extensive randomizations where checking previous seeds takes time. Work in progress. This requires specification of a tree; it never swaps at the end as in noglobal [no]xeven for exclusive sectors, [don't] use sectors of as even a size as possible uneven sectors make it more likely to find better trees if using several rounds minsize N minimum size for random selections maxsize N maximum size for random selections minfork N minimum fork for constraint-based selections maxfork N maximum fork for constraint-based selections increase N factor to increase size if enough selections of current size completed.
Note: for sectors above drift size, the autofuse option of drift applies. If N is smaller than the size to use drift, drift is not done. Number C of drift cycles for each start is determined with drift C, number F of fuses is determined with fuse F.
This is to be used in combination with macro expressions "nodtosect", "biginsect" chkroot for XSS searches only, make sure the base of tree which often may be unselected is included as well; this may actually use one more selection than requested.
TNT, a free program for phylogenetic analysis. Goloboff, Pablo A. The main features of the phylogeny program TNT are discussed. Windows versions have a menu interface, while Macintosh and Linux versions are command-driven. The program can analyze data sets with discrete additive, non-additive, step-matrix as well as continuous characters evaluated with Farris optimization. Farris , Kevin C. Publication date Created: October Publication date Print : October Journal: Cladistics.
Mac 64 — no taxon limit. Linux Linux 64 — no taxon limit. It is a program for phylogenetic analysis under parsimony with very fast tree-searching algorithms; Nixon, , Cladistics ; Goloboff, , Cladistics , as well as extensive tree handling and diagnosis capabilities.
The Willi Hennig Society. As of November , the project was subsidized by the Willi Hennig Society , and thus the program is now made freely available, upon agreement on the terms of the license presented by TNT when it is run for the first time in a machine a copy of the license can be found here. Mixing 32 and 64 bit versions poses no problem, but binaries with limits on number of taxa do not connect properly to binaries without such limit, and viceversa.