Phylogenetic trees made easy: a how-to manual

Read me first!

Tutorial : estimate a tree!

Acquiring

Aligning the sequences

Major methods for estimating phylogenetic trees

Neighbor-joining trees

Drawing phylogenetic trees

Parsimony

Maximum likelihood

Bayesian inference of trees using MrBayes

Working with various computer platforms

Advanced alignment using GUIDANCE

Reconstructing ancestral sequences

Detecting adaptive evolution

Phylogenetic networks

Some final advice : Learn to program

File formats and their interconversion

Additional programs.