- 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?

- 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*?

- 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?

- 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*?

- 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?

- 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?

- 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?

- 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?

- 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?

- 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?

- 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?

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

- 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?

- 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?

- 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"?

- 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)?

- 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?

- 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?

- 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?

- 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?

- 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?