Sunday, September 9, 2007

PAUP Help...

I have been running phylogenies and have been having this problem with PAUP running maximum parsimony where it is supposed to find the 1000 most parsimonious trees.

Elapsed Taxa Rearr. -- Number of trees -- Best
time added tried saved left-to-swap tree(s)
33:22:11 - 247089521 1000 628 223551
33:23:11 - 247154671 1000 627 223546
33:24:11 - 247315353 1000 627 223546
33:25:11 - 247430339 1000 627 223546
33:26:11 - 247587809 1000 627 223546
33:27:11 - 247713071 1000 627 223546
33:28:11 - 247815620 1000 626 223543
33:29:11 - 247946647 1000 626 223543
33:30:11 - 248070084 1000 626 223543
33:31:11 - 248213054 1000 626 223543
33:32:11 - 248347299 1000 626 223543
33:33:11 - 248481072 1000 625 223543
33:34:11 - 248565681 1000 625 223543
33:35:11 - 248698430 1000 625 223543
33:36:11 - 248808469 1000 625 223543
33:37:11 - 248972895 1000 625 223543
33:38:11 - 249090122 1000 625 223543
33:39:12 - 249167303 1000 691 223543
33:22:11 - 247089521 1000 628 223551
33:23:11 - 247154671 1000 627 223546
33:24:11 - 247315353 1000 627 223546
33:25:11 - 247430339 1000 627 223546
33:26:11 - 247587809 1000 627 223546
33:27:11 - 247713071 1000 627 223546
33:28:11 - 247815620 1000 626 223543
33:29:11 - 247946647 1000 626 223543
33:30:11 - 248070084 1000 626 223543
33:31:11 - 248213054 1000 626 223543
33:32:11 - 248347299 1000 626 223543
33:33:11 - 248481072 1000 625 223543
33:34:11 - 248565681 1000 625 223543
33:35:11 - 248698430 1000 625 223543
33:36:11 - 248808469 1000 625 223543
33:37:11 - 248972895 1000 625 223543
33:38:11 - 249090122 1000 625 223543
33:39:12 - 249167303 1000 691 223543

The number of trees left to swap went up and rapidly went from 691 to 975 at last check. Has anyone had that happen? I haven't seen it before and trying to make sense of it. Any help would be greatly appreciated.

Thanks!

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