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Assembling the Tree of Life: Early Bird

Downloads

Downloads and Other Links

The Early Bird project used a wide variety of analytical approaches, some of which were computationally demanding. There were also a number of data management issues that reflect the complexity of the data collected. A number of utilities were written for this purpose by Edward Braun.

A number of programs and scripts written by Edward Braun are available below, as are additional links to programs that were used extensively by members of the Early Bird project and other resources.

Please send any feedback about this web page to Edward Braun. This page includes a number of links to external web sites; we do not maintain those web sites and we are not responsible for the contents of those pages (for more information see the Early Bird linking policy).

Downloads

Programs written by Edward Braun are available for download: (MORE ARE COMING SOON)

  • The “combine” program. A C++ program useful for combining nexus files while retaining charset information. A perl version of this program is being completed and I expect it to be easier to use (it will also add an RY-coding function).
  • The “gappy” program, used to generate charsets that allow columns with specific numbers of gaps (or missing data).
  • Perl programs to simplify renaming taxa in phylogenetic trees, including the Early Bird trees we distribute from this web page.

Additional Links

Links related to Early Bird and other AToL projects are presented below:

  • Information on NSF-supported Assembling the Tree of Life (AToL) projects.
  • There were close interactions between many AToL groups and the CIPRES (Cyberinfrastructure for Phylogenetic Research) groups.
  • Trees and data matrices for many phylogentic projects, including the Early Bird project, have been deposited in TreeBase.
  • The Early Bird group has benefitted from meetings held at NESCent, the National Evolutionary Synthesis Center.
  • Information from the Early Bird project has been incorporated into the bird pages of the Tree of Life (ToL) web project.
  • Many analyses were conducted using the fast maximum-likelihood programs GARLI and RAxML. Many of our analyses also used PAUP*.

The largest list of phylogeny programs available is maintained by the Felsenstein group at the University of Washington. The PHYLIP package for phylogeny inference is also available from this group.