Batch files

[batch file from the Brianmeara page]

#nexus
begin PAUP;
log file=hsearch1.log;
set autoclose=yes;
cstatus;
hsearch start=stepwise addseq=random nreps=100 savereps=yes randomize=addseq rstatus=yes hold=1 swap=tbr multrees=yes;
savetrees file=hsearch1.all.tre;
filter best=yes permdel=yes;
savetrees file=hsearch1.best.tre;
log stop;
end; 



[batch file from PAUP's Quick start]

Begin paup;
set autoclose=yes warntree=no warnreset=no;
log start file=practice.log replace;
execute primate-mtDNA-interleaved.nex;
cstatus;
include coding/only;
undelete hominoids lemur_catta macaca_fuscata saimiri_sciureus/only;
weight 2:1stpos;
ctype 2_1:all;
Set criterion=parsimony;
hsearch addseq=random;
Showtree;
describetrees 1/ plot=phylogram brlens=yes;
savetrees file=mp.tre replace;
set criterion=distance;
dset distance=hky85;
showdist;
nj;
dset objective=lsfit power=2;
hsearch;

gettrees file=mp.tre;
lscore 1/wts=ignore nst=2 tratio=est rates=gamma
shape=estimate;
set criterion=likelihood;
lset tratio=previous shape=previous;
hsearch addseq=asis;
end;


[batch file from http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/Commandblocks.pdf]

Begin paup;
set autoclose increase=auto;

log start file=practice.log replace;

set crit=p;
hsear addseq=rand nreps=10;
savetrees file=pars.tre brlens;
boot nreps=1000 sear=heur;
savetrees file=pars-boot.tre from=1 to=1005;

[paste in results of Modeltest: Lset ...];

set crit=d;
dset dist=ml;
nj;
savetrees file=nj.tre brlens;
boot nreps=1000 sear=nj;
savetrees file=nj-boot.tre from=1 to=1000;

set crit=l;
hsear addseq=rand nreps=1;
savetrees file=ml.tre brlens;
boot nreps=500 sear=heur treefile=ml-sum.tre;
savetrees file=ml-boot.tre from=1 to=502;

End;

This command block sets the memory tree limit to automatic increase (set increase=auto),
performs a parsimony search with bootstrapping (1000 replicates), a distance analysis with
neighbor- joining and maximum likelihood settings, a distance/nj bootstrap analysis (1000
replicates) and a maximum likelihood analysis with bootstrapping (500 replicates). After each analysis step, the resulting tree is saved to a file.




1. Open and execute file

2. File > Log Output to Disk...

3. cstatus;  summary of the current character status (i.e., types, weights,etc.)
      tstatus  - summary of the taxa 
   showmatrix - show the entire data matrix

4. set criterion=parsimony ou distance ou likelihood,
para escolher o método

5. dset escolhe a distance dset distance= 
escolher bootstrap ou jackknife 

basefreqs dá  as frequências das bases
factory restaura os defaults
outgrope n£mero n£mero... forma um outgroup com os taxa numerados.
ingroup n£mero n£mero.... traz para o ingrupo os taxa indicados pelos n£meros.
showtrees e describetrees fornecem informações sobre as árvores que são importantes para a redação dos trabalhos
Para gravar resultados, usar no paup log file=file name.
Para interromper, fazer log stop
Para reiniciar log start
Log start append, continua a usar um ficheiroanterior.

Hsearch nbest=n onde número inteiro, de árvores a guardar na memória.
Grava as n melhores árvores.
para as ver, usar depois sorttrees para serem ordenadas e depois describetrees com lista
de números por exemplo: 1 2 3 ...

Use the HOMPART command to perform test for homogeneity of 
partitioned data sets. This test was described as the incongruence-length
difference test by Farris et. al. (1995). The syntax is: 
HOMPART [ options ] [/ heuristic-search-options | branchand-bound-search-options ] ; 
Available options: 
Default setting Option type 
character-partition-name PARTITION - 
July, 1998 PAUP* 4.0 beta documentaion 64
Commands used in the PAUP Block Command Reference 
integer-value 100 NREPS 
integer-value SEED 0
HEURISTIC { HEURISTIC | BANDB } SEARCH 
Description of options: 
PARTITION = character-partition-name 
Use PARTITION to specify the character-partition-name to be used in

the analysis. To learn how to setup Character-partitions see 
CHARPARTITIONS page 23. 
exemplo hompart partition=nome

NREPS = integer-value 
Use NREPS to specify the number of homogeneity replicates to be 
performed. 
SEED = integer-value 
By default, PAUP* references the system clock to obtain a value used

to seed a random number generator. An explicit seed may be 
specified to override the system clock default. (See "InitSeeds = {
0 | 
1 }" on page 106 for more details.) 
SEARCH = { HEURISTIC | BANDB } 
A search is performed for each data partition replicate using the 
option specified for SEARCH. Options for either of the search 
options may be specified after a slash. (See the "BandB" command 
described on page 36 and the "HSearch" command described on page 
65 for a description of the available options.) 

    Para obter as dist¦ncias entre taxa, proceder assim:
Primeiro: set criterion=distance.
Depois, escolher a dist¦ncia com dset distance=....
Fazer o bootstrap.
Finalmente, executar o comando: savedist file="file name".

CHARPARTITION, TAXPARTITION 
These commands define partitions of characters, taxa, and trees, 
respectively. The partition divides the objects into several (mutually

exclusive) subsets. They follow the same format, and will be described

together. 
There are several formatting options. The VECTOR format consists of
a list of 
partition names. By default, the name of each subset is a NEXUS word
(this 
is the TOKENS option). The NOTOKENS option is only available in the
VECTOR 
format; this allows one to use single symbols for the subset names.
Each 
value in a definition in VECTOR format must be separated by whitespace
if 
the names are tokens, but not if they are NOTOKENS.
exemplo charpartition nome=1:1-500, 2:501-1039; 
para definir propor‡„o de ts/tv,fazer no
ficheiro no assumptions block,
um comando do tipo usertype com a matriz de pesos
depois, na linha de comando, fazer typeset =nome:
No exemplo do ficheiro test.nex, um peso de
3/1 ‚ definido no usertype abelha.
Neste caso fazer typeset tipo=abelha: onde
tipo ‚ o nome a dar ao typeset.
Para isto ser assumido usar
o comando assume.
Neste caso assume typeset=tipo.


	Para impor constrangimentos,indicar no bloco de assumptions os taxa a juntar. Ver as
constraints ch and chg no ficheiro test.nex
Depois para escolher uma, usar o comando set na forma set constraints=nome, no caso ch ou chg
depois antes do bootstrap executar o comando hsearch enforce=yes

What are topological constraints?

Topological constraints are unresolved trees used to filter out trees discovered during the search that do not match a particular topological criterion. One possible use of a topological constraint is to force a particular group to be convex (i.e., monophyletic if the tree is rooted outside the group). This type of topological constraint is referred to as a monophyly constraint. Monophyly constraint trees contain all the taxa but are unresolved to some degree. A second type of constraint is called a backbone constraint. Backbone constraint trees are normally fully resolved, but are missing one or more taxa. A tree encountered during a search is consistent with a backbone constraint tree so long as pruning all taxa not in the constraint tree yields the constraint tree topology. One may wish to compare the support of the data for the best tree obtained under the constraint to the best tree without the constraint. Note that PAUP* offers much more flexibility in terms of topological constraints than is indicated here; the manual for version 3.1 explains constraints thoroughly. 

How do I define and name a topological constraint?

Suppose you are studying bot flies that parasitize either lagomorphs or rodents depending on the species. You may be interested in finding the best tree in which the lagomorph-infecting species of bot flies form a monophyletic group. Assume that there are 10 taxa, and taxa 2, 3, 5, 7 and 9 are lagomorph-infecting species, while the others (1, 4, 6, 8 and 10) are rodent-infecting species. 
constraints lagomorph (monophyly) = (1,4,6,8,10,(2,3,5,7,9));


Here, the word lagomorph is the name of the topological constraint, and the word monophyly is a keyword indicating the type of constraint (the other possible type is specified using the keyword backbone). Note that taxa connected directly to the root node do not have to be specified explicitly in constraint-tree definitions, and monophyly constraints are the default. The above example could thus also be written: 
constraints lagomorph = ((2,3,5,7,9));


How do I load a topological constraint in the form of a tree file?

Suppose one or more constraint trees exist as tree definitions in a tree file named "foo.tree" (the names of the trees in the tree file will become the names of the corresponding constraint definitions when the treefile is loaded). 
loadconstr file=foo.tree;


If the trees in "foo.tree" are to be considered backbone constraints, then the keyword "asbackbone" must be included (otherwise the trees are considered to be monophyly constraints): 
loadconstr file=foo.tree asbackbone;