Quantitative Phylogenetics

PAUP* Command Glossary
(a complete manual of PAUP* commands
can be downloaded here)

 


Basic commands

To read a data file into PAUP*,
Execute filename;
[make sure the data is in the home directory]

To create a log file of everything that is sent to the console:
Log file = filename;

To define a constraint to conserve monophyly of a taxon:
constraint "name" (monophyly) = ((taxon_1, taxon_2, …, last_taxon));
where "name" is whatever you want to call this particular constraint

To have PAUP* show you what it thinks the currently defined constraint statements mean:
showconstr all;

To collapse branches with minimum branch length of zero:
Condense collapse=minbrlen;

To set the optimality criterion:
Set criterion= *** ;
where *** is parsimony, distance, or likelihood

To include or exclude a set of characters, previously defined:
Exclude Character-set-name;
Include Character-set-name;


Searches and Branch-Swapping

To conduct a branch and bound search:
BandB;

To conduct a branch and bound search with negative constraints:
BandB enforce=yes constraints=name converse=yes;

Conduct a heuristic search, 100 random addition sequences followed by TBR branch-swapping
Hsearch start=stepwise addseq=random Nreps=100 swap=TBR;

To branch-swap on a tree or trees in memory:
hsearch start=current swap=TBR;

To conduct a bootstrap analysis using Branch and Bound searches:
bootstrap nreps=100 search=bandb;


Distance commands

To set the molecular distance method:
dset distance = ***;
where *** is one of the following: P, JC, F81, K2P, F84, HKY85, K39, GTR, etc.

To output the matrix of distances to an external file:
SaveDist format=onecolumn file=filename;
Other possible formats are TabText, Nexus, Phylip

To print the distance matrix in the output log:
ShowDist;

To eliminate negative branch lengths:
dset NegBrLen = ***;
where *** is one of the following: prohibit, allow, setzero, SetAbsVal;

To use the minimum evolution criterion:
dset objective=me;
[another possibility is LSFit, for a least-squares approach]

To conduct neighbor-joining clustering:
NJ;

To conduct UPGMA clustering:
UPGMA;


Likelihood commands

To output likelihood scores and parameter estimates for tree(s) in memory:
lscores tree-list;

Commands to set likelihood parameters for common models:

[ GTR + SS3]
lset nst=6 rmatrix=estimate basefreq=estimate rates=sitespec siterates=partition:by_codon

[GTR model]
lset nst=6 rmatrix=estimate rclass=(a b c d e f) basefreq=estimate rates=equal pinvar=0

[GTR+G model]
lset nst=6 rmatrix=estimate rclass=(a b c d e f) basefreq=estimate rates=gamma shape=estimate pinvar=0

[GTR+G+I model]
lset nst=6 rmatrix=estimate rclass=(a b c d e f) basefreq=estimate rates=gamma shape=estimate pinvar=estimate

[TIM2+G model]
lset nst=6  base=est  rmat=est  rclass=(a b a c d e) rates=gamma shape=estimate  pinv=0

[TrN+G model]
lset nst=6  base=est  rmat=est  rclass=(a b a a c a) rates=gamma shape=estimate  pinv=0

[TIM1+G model]
lset nst=6  base=est  rmat=est  rclass=(a b c c d a) rates=gamma shape=estimate  pinv=0

[TIM3+G model]
lset nst=6  base=est  rmat=est  rclass=(a b c a d a) rates=gamma shape=estimate  pinv=0

[JC model]
lset nst=1  base=equal  rates=equal  pinv=0

[K2P model]
lset nst=2  base=equal  tratio=est  rates=equal  pinv=0 

[HKY85 model]
lset nst=2  base=est  tratio=est  rates=equal  pinv=0


Working with Trees

Tree lists, as used with other commands (treelist below):
all = all trees in memory
X = tree X only (X is an integer)
X-Y = trees X through Y, inclusive (X and Y are integers)

To set the outgroup to these taxa only:
Outgroup taxon_1 taxon_2 … last_taxon / only;

To control rooting of trees output to the display or a file:
RootTrees outroot= ***;
where *** is polytomy, paraphyl or monophyl [note, no "y" on end of last two]

to save a treefile:
Savetrees file=filename;
[will put the file in the home directory]

to save a treefile with branch lengths:
Savetrees file=filename brlens=yes;
[will put the file in the home directory]

To read trees into PAUP*:
Gettrees file=filename;

To describe a tree in the output log:
DescribeTrees treelist / plot=***;
where *** is none, cladogram, phylogram or both;
note: many other options are available for this command, including:
BrLens - produces a table of branch lengths, with minimum and maximum values
ApoList - produces a list of characters that change in each interval, keeping track of which state changes are ambiguous and which are unambiguous
ChgList - produces a list of characters, their unit C.I. values, and where each state change occurs in the tree

To construct a strict consensus tree:
Contree treelist / strict=yes majrule=no treefile=filename;

To construct a majority-rule consensus tree:
Contree treelist / strict=no majrule=yes treefile=filename;