The main difference between the two categories are found in the cable specifications, where CAT6 provides higher specs and is therefore preferred in high speed networks. The more 'twists per inch' and higher quality shielding allows CAT 6 cable to be more tolerant in noisy environments where electrical interference is a problem.
Both cables run upto 100 meters, even though CAT 6 can manage more than that – it's advised to keep it to the 100 meter length. Speeds of 1000 Mbps are easily obtained with both cables, but due to the high frequency used, it is always best to use the higher insulated CAT 6 cable.
In short, if you'll be running short distances and speeds upto 100Mbps, CAT5e is probably the best solution when taking into consideration the performance/value factor. If on the other hand greater speeds are required, then look straight for CAT6 cable to avoid future problems.
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