Quantitative PhylogeneticsPAUP* 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 constraintTo 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 likelihoodTo include or exclude a set of characters, previously defined:

ExcludeCharacter-set-name;

IncludeCharacter-set-name;

Searches and Branch-SwappingTo 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 commandsTo 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=Other possible formats arefilename;

TabText, Nexus, PhylipTo 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 isLSFit, for a least-squares approach]

To conduct neighbor-joining clustering:

NJ;To conduct UPGMA clustering:

UPGMA;

Likelihood commandsTo output likelihood scores and parameter estimates for tree(s) in memory:

lscorestree-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 TreesTree lists, as used with other commands (

below):treelist

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 *** ispolytomy, paraphylormonophyl[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=filenamebrlens=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:

DescribeTreestreelist/ plot=***;

where *** isnone, cladogram, phylogramorboth;

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:

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

Contreetreelist/ strict=no majrule=yes treefile=filename;