The alternative to transposition is substitution. Four examples of simple substitution ciphers can be explored by choosing the menu bar options on the left.
The first documented use of a substitution cipher for military purposes appears in Julius Caesar's "Gallic Wars". Caesar describes how he sent a message to Cicero, who was besieged and on the verge of surrendering. The substitution replaced Roman letters with Greek letters, rendering the message unintelligible to the enemy.
Caesar described the dramatic delivery of the message: "If he could not approach the camp, the messenger was instructed to hurl a spear into the entrenchment of the camp, with the letter fastened to the spear's thong…. Fearing danger, the Gaul discharged the spear, as he had been instructed. By chance it stuck fast in the tower, and for two days was not sighted by our troops; on the third day it was sighted by a soldier, taken down, and delivered to Cicero. He read it through and then recited it at a parade of the troops, bringing the greatest rejoicing to all."
Caesar used secret writing so frequently that Valerius Probus wrote an entire treatise on his ciphers, which unfortunately has not survived. However, thanks to Suetonius's "Lives of the Caesar's LVI", written in the 2nd century AD, we do have a detailed description of one of the types of substitution cipher used by Caesar. You can see how this cipher works, on the next page.