Hi,

Yesterday I tried to perform a bootstrap analysis with 1000 replicates using PAUP* on Windows 7. My dataset consists of 107 coding sequences, which has 675 letters each. Frist I used jModeltest to select the best-fit model, and then appended the following PAUP block to DATA block, and excecuted it using PAUP concole.

BEGIN PAUP; log start=yes file=test.log replace=yes; set criterion=likelihood; lset base=(0.3037 0.2083 0.2478) nst=6 rmat=(1.4346 9.4669 0.8990 0.3065 7.1675) rates=gamma shape=0.6360 ncat=4 pinvar=0; bootstrap nreps=1000 bseed=12345 conlevel=60 treefile=bootstrap.tre replace=yes format=NEXUS search=HEURISTIC; savetrees brlens=yes savebootp=both maxdecimals=0 from=1 to=1 file=boots.tre replace=yes; log stop; END;

But it turns out that 17 hours passed, it's in Bootstrap replicate 6 stage. Each run takes more than 3 hours.

So, any wrong in the commands? Or is it just simply a fact that when the number of sequences is above a certain naumber, such as 100, PAUP* is not recommended to use?

Thank in advance for your answer and help!

Thanks. I will give Phylip a try.

When I read papers, I've noticed that most of them use PAUP* to construct a ML tree with 1000 bootstraps. In some cases, their dataset is large, too. So, I'm just curious how they did it...

They will use PAUP too, but the performance is identical to what you're getting. In some tests I made (some years ago) to generate 1000 bootstrap replicates of a 100 taxa matrix, it took more than two weeks.