PAUP* FAQ: Questions

Last updated 22 February 2007

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Questions about the PAUP* FAQ

• Why are all the answers given in terms of commands and not menu choices?
• If I don't find it here, does that mean that it doesn't exist?
• Can I submit questions that I think should be part of this FAQ?

General questions

• I just updated PAUP* using the updater on your web site, yet when I try to run PAUP I still get the message that PAUP* has expired.?
• Is PAUP* Year 2000 Compliant?
• What is a batch file?
• I'm using a beta version of PAUP* 4.0. How should I cite the program?
• Is there a version of PAUP* that will run a search in parallel on a multiple processor machine or a cluster of machines?
• Could you recommend some text books that will help me to learn more about the analyses that can be done in paup?
• What are the maximum dimensions (i.e., characters x sequences) of a data matrix that PAUP* will read?
• What is the maximum number of character states that can be assigned to a character in PAUP*?

Setting the optimality criterion:

• Why doesn't PAUP* allow me to set the criterion to likelihood after I execute my data set?
• How do I tell PAUP* I want to use the likelihood criterion?
• How do I tell PAUP* I want to use the parsimony criterion?
• How do I tell PAUP* I want to use the minimum evolution criterion?
• How do I tell PAUP* I want to use the least-squares criterion?
• How do I tell PAUP* I want to use unweighted least-squares criterion?

Importing non-NEXUS file formats:

• Which non-NEXUS file formats will PAUP* import?
• Where can a find examples of non-NEXUS file formats that PAUP* will import?
• How do I import non-NEXUS formatted files into PAUP*?

Deleting and restoring taxa, excluding and including characters (sites):

• How do I tell PAUP* to ignore certain taxa in further analyses?
• How do I tell PAUP* to use taxa that I previously told it to ignore?
• How do I tell PAUP* to ignore certain characters (sites) in further analyses?
• How do I tell PAUP* to use characters (sites) that I previously told it to ignore?
• How do I exclude all the constant characters?
• How do I exclude all constant as well as autapomorphic characters?

Combing data sets

• How do I combine different data set into a single NEXUS file?
• How do I code indels so that they are not treated as missing data?

Creating data partitions:

• What are data partitions and why are they useful?
• How do I define and name a data partition?
• How do I do a partition homogeneity test?

Defining and using topological constraints:

• What are topological constraints?
• How do I define and name a topological constraint?
• How do I load a topological constraint in the form of a tree file?
• How do I apply a previously-defined topological constraint to a search?

Tree files:

• How do I get a single majority-rule bootstrap consensus tree from the results of multiple bootstrap runs performed at different times or on different machines?
• How do I tell PAUP* to save the trees currently in memory to a file?
• How do I tell PAUP* to read in trees previously saved in a file?
• Why can't I get PAUP* to save branch length on the bootstrap consensus tree?

Questions about searching

• How can I limit the number of rearrangements PAUP* evaluates during a heuristic search?
• Why are fractions listed in the bootstrap bipartition table when 100 bootstrap replicates are performed?
• How do I ask PAUP* to examine every possible tree topology?
• How do I evaluate 500 random-addition replicates but prevent PAUP* from branch swapping on each one?
• How do I set a maxtree limit for each random addition sequence replicate?
• I have performed an heuristic likelihood search and specified 100 replicates within the hsearch command. When I examine the progress reports, it looks like PAUP* is finding many different tree islands, however the summary at the end says that only one island was found and that island was hit 100 times. What is going on here?
• Do you have equations for estimating the relative (or actual) time required for heuristic searches for sequences of different length and for different numbers of sequences?

Questions about PAUP* interfaces

The Macintosh Interface

• Is there a version of PAUP* that will work on my new Intel-based Mac?
• Is there a version of PAUP* that will work natively under Mac OS X?
• I just purchased a new Mac and Classic support is not installed on the system. How do I run PAUP* without classic support?
• I get an error when I try to print from the classic version of PAUP*. How do I print from the classic version of PAUP*?
• How do I increase the amount of memory available to PAUP*?
• Can I download a Mac updater to a PC and transfer the updater to a Mac that is not online?
• How do I tell PAUP to automatically close the heuristic search status window at the end of the search?

The DOS Interface

• How do I keep information from scrolling off the screen before I have read it?
• How do I recall a PAUP* command?

The Windows Interface

• How do I print trees using the Windows Interface?

Questions about parsimony

• How does PAUP* deal with missing characters under the parsimony criterion?
• What options are available in PAUP* for dealing with multi-state taxa?
• How do I define multistate characters as ordered in PAUP?
• If a patristic distance is the sum of branch lengths on a path between a pair of taxa, why do the summed branch lengths between a pair of taxa not add up to the patristic distance reported under the "describetrees" command?
• I did a search under the parsimony criterion and got two trees that look just alike. Why does PAUP consider them to be different?

Parsimony-based tests

• How do I perform a Kishino-Hasegawa test to see if the support for the first and second trees stored in memory is significantly different?
• How do I perform a partition homogeneity (congruence) test?

Weighting Characters

• How do I downweight third position transitions only in a parsimony analysis?
• How do I weight specific character positions in my alignment?
• Do stepmatrices for character state transformations have to be symmetric?
• Why does PAUP* tell me that my stepmatrix violates the triangle inequality?
• Why does PAUP* warn me that the stepmatrix supplied in Xu and Miranker (2004, "A metric model of amino acid substitution", Bioninformatics 20:1214-1221) is "internally inconsistent"?

Goodness-of-fit Statistics

• What do the indices under the "pscores" command mean?

Questions about likelihood

• How does PAUP* deal with missing characters under the likelihood criterion?

Selecting substitution models

• How do I tell PAUP* I want to use the JC69 model (Jukes & Cantor, 1969)?
• How do I tell PAUP* I want to use the K2P model (Kimura, 1980)?
• How do I tell PAUP* I want to use the F81 model (Felsenstein, 1981)?
• How do I tell PAUP* I want to use the F84 model (i.e., the model used in DNAML)?
• How do I tell PAUP* I want to use the HKY model (Hasegawa, Kishino, & Yano, 1985)?
• How do I tell PAUP* I want to use the GTR model (i.e., the general time reversible model)?

Likelihood scores

• How do I obtain likelihoods for all trees in memory?
• How do I obtain likelihoods corresponding to each individual nucleotide site in my data using the first tree in memory?
• How do I force PAUP* to use the branch lengths I specify when computing site likelihoods?
• How do I perform a Kishino-Hasegawa test to see if the support for the first and second trees stored in memory is significantly different?

Transition/transversion ratio

• What is the difference between the transition/transversion ratio and the transition/transversion rate ratio?
• How do I tell PAUP* to estimate the transition/transversion ratio when using the HKY substitution model?

Rate heterogeneity

• How do I take account of rate heterogeneity across sites using a discrete gamma distribution, four rate categories, and a shape value of 0.2?
• How do I estimate the shape parameter when I am using a four-category discrete gamma distribution to account for heterogeneity in rates across sites?
• How do I tell PAUP* to estimate the proportion of invariant sites?
• How do I tell PAUP* to assume there are no invariant sites?
• How do I tell PAUP* to estimate the proportion of invariant sites and and estimate the shape parameter of a discrete, four-category gamma distribution applied to the sites that are not invariant?
• I think most of the rate heterogeneity in my sequences are the result of codon structure. How can I tell PAUP* to assume a different rate for each codon position (i.e., estimate site-specific rates)?
• How do I tell paup to use site-specific rates that I have already estimated?
• When I estimate the shape parameter of the gamma-distributed rates model and the proportion of invariable sites simultaneously, PAUP tells me that pinvar is zero even though the empirical number of invariable sites is about 30 percent. Why?

Ancestral States

• How do I get the relative probabilities for each ancestral base assignment?

Questions about distance

• How do a import a pairwise distance matrix from another program into PAUP*?
• How does PAUP* distribute missing or ambiguous changes proportionally to unambiguous changes?

Examples of paup blocks for conducting entire analyses

• We need to do a likelihood search on a UNIX machine with a general time reversible model (I+Gamma), i.e. some sites assumed to be invariable with gamma distributed rates at variable sites, with a heuristic search with 10 repetitions random addition taxa and TBR branch swapping
?
• I have a sequence data set for which I would like to infer the phylogeny. What is a sequence of analyses that I can perform that will cover most potential pitfalls I am likely to encounter?