Scripts
From TNT
Revision as of 20:12, 28 March 2012 by Sacatalano (Talk | contribs)
See also How do I run a script?, Scripting Help and Scripting Commands.
Script archive
When using the script template on the wiki do not leave semicolons (;) alone on a line, they will not be correctly rendered.
Click on the title to see further explanation, including required parameters.
| title | usage/function/purpose | script file(right-click, save as) | |||
|---|---|---|---|---|---|
| Bremer support | Calculates Bremer support. Easy to use given its nice interactive window. | Bremer.run | |||
| Partitioned Bremer support | Calculates partitioned Bremer support. By Carlos Peña. | Pbsup.run | |||
| aquickie | A script to perform a simple one-shot analysis, ideal for new or lazy TNT users . This runs a simple analysis with a search for most parsimonious trees (or asks whether you want to do a consensus estimation, if the data set is large), then calculates group supports using resampling. | aquickie.run | |||
| stats | Calculates RI and CI. [NOTE added by Nick Matzke: Stats.run seems to crash if you have more than about 400 trees in memory. i.e. after "hold 400; mult 100 =tbr drift ;" works, but after "hold 500;" it doesn't.] | Stats.run | |||
| TTS | Calculates the number of three-taxon statements implied by the first tree that are true on the second tree. | TTS.run | |||
| Term lengths | This script finds the taxa which increase tree length the most (reporting ties when they exist). | Term_lengths.run | |||
| RF_Distances | This script calculates the Robinson-Foulds distance between two trees given as arguments | RF_Distances.run | |||
| Implied_weighting | This script defines a (user-defined) number of K, under implied weighting (IW), that produce even intervals of fit/distortions, analyzes the matrix under IW using these values of K, and make some comparisons between the results obtained under different K-values (to evaluate stability of results across evenly differing analytical conditions). More details in Mirande (2009) | Implied_w.run | |||
| LandschW | This script allows to run searches considering (exclusively) landmark data. It generates a Wagner tree (RAS) and swaps it using TBR. It receives only one argument, that is the level of thoroughness of the analysis ( 0 is the lowest, 4 is the highest). If no argument is given the script will run a seach departing from a single Wagner tree and considering the current settings for landmark optimization. (This scripts replaces the original script landsch.run where each run departed for a random tree) | LandschW.run | |||
| Landcombsch | This script allows running tree searches combining landmark data with other sources of evidence. Each replicate starts from a Wagner tree (RAS)followed by TBR. Only a single optimal tree is kept in memory.
You should specify one argument: 1st = strength of the search (modifies the number of replicates and precision in landmark optimization(0: lowest (fast) , 4: highest (slow). Default = 0) | Landcombsch.run | |||
| export_tps | This script export to TPS format the landmark coordinates of terminals and inner nodes of the first tree in memory. It produces one file for each lm configuration. Besides it generates a tree drawing with the numbers of the inner nodes corresponding to the names given in the TPS file | export_tps.run | |||
| mytaxo | This is the script used in Goloboff et al., 2009. See paper for details of usage. The script checks groups (calculating their fit on multiple trees), also finding taxa to prune to improve groups. First argument is max. depht, second argument is group to improve (both are optional). It stores taxa to prune in group 31 (if doing only a group, it stores taxa to cut to improve that group, to the level specified) | mytaxo.run | |||
| colorgroups | This is the script used in Goloboff et al., 2009. The script colorgroups.run (for Windows only) will take a list of taxa and automatically produce color diagrams displaying the groups. If you wish to use the same color code for several separate groups, you can separate the groups to be given similar color with a plus and a colon, and the groups to be given different colors with blank spaces; for example:
colorgroups _Araneae_+:_Nematoda_ _Diptera_+:_Porifera_ will give spiders and nematodes one color, and sponges and flies another. The figures produced with this script can be exported as metafiles. | colorgroups.run | |||
| blens | This macro plots phylograms | blens.run | |||
| dohi | This is the script used in Goloboff et al., 2009.It takes as argument the name of a group, so that:
dohi _Mammalia_; will find the group in the tree most similar to ‘‘Mammalia’’, and display it on screen (counting the number of non-members included, and of members excluded). | dohi.run | |||
| blockboot | performs Siddall's (2010) partition bootstrap | blockboot.run | |||
| blockjak | performs Siddall's (2010) partition jackknife | blockjak.run | |||
| Codonweight | allows reweighting of 1st, 2nd and 3rd positions for a scope of characters | Codonweight.run | |||
| ILD | Incongruence Length Difference Test of Farris et al 1995 | Ild.run | |||
| deactmiss | Deactivate taxa with a given amount of missing data | Deactmiss.run | |||
| excludemiss | Excludes characters that are missing for a given percentage of taxa | Excludemiss.run | |||
| forall | Finds all files (recursively traveling subdirectories) which match a file name. | forall.run | |||
| example | An example script/template that can be copy pasted for other scripts presented here. | none' |
