In this article Robert O'Hara brings the philosophy of history to bear on "discussions of the theory and practice of systematics and evolutionary biology". Part of his analysis draws sharp distinctions between the idea of a chronicle and narrative history. He also explores the difference between non-evolutionary questions about the "states" of characters and evolutionary questions about "changes" in characters. Both html and PDF versions of the article are available on-line.

Quote from source: The ability to analyze evolutionary “why” questions in this way comes from what I call “tree thinking” (after Mayr’s “population thinking”). Tree thinking is absolutely necessary for answering almost all evolutionary “why” questions. A pre-evolutionary perspective on diversity results in what may be called “group thinking,” and state questions arise out of group thinking; it is tree thinking that allows one to convert a question of state into an evolutionary question of change.

This huge annotated and cross referenced list of phylogenetics tools is maintained by Joseph Felsenstein at the University of Washington. Some of the listed software is free and available on the web while others are commercial tools that require licensing. You might want to consider the free programs PHYLIP - for building trees, and Phylodendron - for drawing trees.

Quote from source: Here are some 194 of the phylogeny packages, and 18 free servers, that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made about twice a year.

A substantive introduction to the shift in perspective associated with tree thinking.

Quote from source: Two new modes of thinking have spread through systematics in the twentieth century. Both have deep historical roots, but they have been widely accepted only during this century. Population thinking overtook the field in the early part of the century, culminating in the full development of population systematics in the 1930s and 1940s, and the subsequent growth of the entire field of population biology. Population thinking rejects the idea that each species has a natural type (as the earlier essentialist view had assumed), and instead sees every species as a varying population of interbreeding individuals. Tree thinking has spread through the field since the 1960s with the development of phylogenetic systematics. Tree thinking recognizes that species are not independent replicates within a class (as earlier group thinkers had tended to see them), but are instead interconnected parts of an evolutionary tree. It lays emphasis on the explanation of evolutionary events in the context of a tree, rather than on the states exhibited by collections of species, and it sees evolutionary history as a story of divergence rather than a story of development. Just as population thinking gave rise to the new field of population biology, so tree thinking is giving rise to the new field of phylogenetic biology.

This on-line lecture by Steven Nadler at the University of California, Davis provides a basic introduction to phylogeny and the inferences made during tree building. It was presented as part of a course held at the Huso Biological Station, Abo Akademi University in Aland, Finland, in 2001.

Quote from source: By the 1970's, tremendous progress had been made in both the theory and practice of phylogenetics. "Tree-thinking" -- using phylogenetic trees as investigative tools -- is now a common research theme in all fields of biology. Open any issue of a biological journal (where research results are reported) and you are sure to find phylogenetic trees being used to understand biological processes. Therefore, it is essential for you to have an understanding of the basic elements of phylogenetic trees -- such as how they are constructed and interpreted. This handout will cover 2 topics: I. Tree terminology - providing basic information for understanding and interpreting phylogenetic trees. II. Tree inference - 1 example of how trees are constructed and used to study character evolution.