Consense gives wierd branch lengths! How do I get more reasonable ones?
Consense gives branch lengths which are simply the numbers of replicates that support the branch. This is not a good reflection of how long those branches are estimated to be. The best way to put better branch lengths on a consensus tree is to use it as a User Tree in a program that will estimate branch lengths for it. You may need to convert it to being an unrooted tree, using Retree, first. If the original program you were using was a parsimony program, which does not estimate branch lengths, you may instead have to make some distances between your species (using, for example, DnaDist), and use Fitch to put branch lengths on the user tree.
