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Pokerstove gives you pot equity and not probability of winning. In some cases this may cause the probability of winning be like 2% but pot equity will be like 49%, because if the split of the pot.
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Actually, PokerStove gives the probability of winning, too. See the text box at the bottom of the window, e.g.,
<ul type="square">
Text results appended to pokerstove.txt
1,712,304 games 0.032 secs 53,509,500 games/sec
Board:
Dead:
<font color="white">...........</font>equity
win tie pots won pots tied
Hand 0: 47.508%
02.17% 45.33% 37210 776269.00 { AcKd }
Hand 1: 52.492%
07.16% 45.33% 122556 776269.00 { AhKh }[/list]
The tie percentage is actually not the percentage of ties, but your equity from ties.