The tool you need really depends on what job you're trying to do. Based on your description, it sounds like you want topological sorting and critical path analysis.
Topological sorting is the 'what comes before what else?' stage of planning. IMO, the best toolset for that is a couple of good-sized whiteboards and a pad of 3x5 post-it notes.
Start with a randomly-selected step in some process. Write the name of that step across the top of a post-it note. Draw a line under the name, then a vertical line splitting the lower part of the note in half. On the left, write all the things this step needs before it can happen. On the right, write all the things this step produces. Stick the note to the whiteboard, and draw a line away from the card for each 'consumable' and each 'deliverable'. Make notes for the stages that produce or consume each item, and paste those at the end of the appropriate line. Repeat until every line has a note at both ends.
That's your process graph. Don't worry about making it pretty, but try to keep it from becoming too much of a haystack. If at any point you decide you need to rearrange things, move the post-it notes to the other whiteboard one at a time, redrawing connections as necessary.
Once your process graph is complete, you can sort it topologically, which just means putting things in the order of their dependencies.
Start by circling all the notes that have no incoming connections (self-contained steps). For each circled note, draw a large dot in the center of each line that comes out from it. Once all the lines are dotted, move the note to a column running down the left side of your second whiteboard, which for convenience I'll call the 'sorting board'.
Go back to the process graph, and this time circle the notes whose incoming edges all have dots (all the dependencies for this step have already been moved to the sorting board). Draw dots on all those outgoing edges, move all the notes to a second column on the sorting board, and draw all the connections from column one to column two.
Repeat that 'find the notes whose inputs are all dotted, dot their outputs, move them to the sorting board, draw connections' process until all your notes have moved over to the sorting board. Now you have a well-organized graph of what comes first and what comes next. Each column is a 'stage' of production.. a set of operations you can do in parallel.
To do a critical path analysis, start with the notes in column one (all the way to the left) and write a number on each note that tells you how long that step will take once you have all the stuff you need. Copy that number onto each edge leaving that note. When you're done with the last note in column one, find the line or lines that have the largest number and draw a dot on the center of those lines. Those are your 'critical' (slowest) connections. Copy the largest number to the bottom of the board below column one. That's your 'critical deadline' for that stage. You can delay any step in a stage as long as you don't exceed the critical deadline.
Next, go to column two. Write a time value on each note, then look at all the lines coming into that note and pick the one with the highest number. Add the highest incoming number to the number on the note itself, and write the sum on every line coming out from the note. Again, when you get to the end of the column, find the line or lines with the highest number, put a dot on them, and write that critical deadline at the bottom of the board below column two.
Repeat that process all the way to the last column. When you're done, there will be at least one path from the first column to the last one with a dot on every line. That's your critical path.. the slowest path through the process, and the one that will hurt you the most if anything goes wrong. You'll also have a row of critical deadines across the bottom of the board that you can use as milestones during the process.
Honestly, I find it easier to do the whole thing with office supplies than to try doing it in software.
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