Here are 392 phylogeny packages and 54 free web servers, (almost) all 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 roughly monthly. Here is a "waiting list" of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from ftp server machines. The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. Email addresses in these pages have had the @ symbol replaced by (at) and also surrounded by invisible confusing tags and blank characters in hopes of foiling spambots that harvest email addresses. ... by methods available ... by computer systems on which they work ... cross-referenced by method and by computer system. ... by ones which analyze particular kinds of data.
Related: Mind Maps/Thinking Maps/Graphic Organizers