Phylomatic Documentation

Version 3

Source

Sending data with curl

curl is a handy command line tool for interacting with websites. You can send the data from a web-form back to the server from curl, if you know the parameters. The easiest way to use this to send data to phylomatic is first to create a text file (e.g., phylomatic.dat) with the parameter data:

      storedtree=R20120829&informat=newick&method=phylomatic&
      taxaformat=slashpath&outformat=newick&
      taxa=acanthaceae%2Fbravaisia%2Fbravaisia_sp1%0D
      acanthaceae%2Fsuessenguthia%2Fsuessenguthia_sp1%0D
      ...
      %0D
    

Note that there should be no line-breaks in your input file. The whole thing should be one long string of text. The %2F and %0D symbols are URL-encoded slashes and newline characters, respectively. Then just send the data to te server with:

      $ curl -d @phylomatic.dat http://phylodiversity.net/phylomatic/pmws > output.new
    

(The > output.new redirects the output to a file)

Too many taxa for this online version of phylomatic?

If you have more than about 5,000 taxa, a job on this server will take too long and the gateway will timeout. A limit of 5,000 taxa has now been placed on a taxa file. You have two alternatives:

  1. Use the desktop version of phylomatic, available with phylocom, or
  2. Use this (gawk-powered) version of phylomatic on your own computer:
    1. Aquire the files from github.
    2. Make sure the first line of the pmws file points to your gawk (version >= 4.0) executable.
    3. Run with (for example):
      $ echo "informat=newick&storedtree=R20120829&method=phylomatic&taxauri=http://foo.com/bar.new&outformat=newick&local=1" \
        | path/to/pmws > out.new
    

(Note the local=1 switch!)

Acknowledgements

Previous phylomatic versions