You can try the Kowalski Simulator.
It has is own assembler and debugging tools. You can view memory and registers, use breakpoints and single step. I have made some corrections to the cycle counting and fixed a few other bugs as well.
My latest release is here:
viewtopic.php?f=8&t=5011&hilit=kowalski#p60014I have used it to develop several timing critical applications, most recent was the 6502 badge that used a bit banged serial output and the IRQ pin as the serial input. A modified badge was also given to Chuck Peddle which was a date and time clock that also counted the number of days since the 6502 was created, and had several scrolling factoids about the 6502. All was being driven completely with cycle counting for keeping the clock updated. See more about the badge here
http://www.sunrise-ev.com/6502.htmDaryl
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https://sbc.rictor.org/