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Phylomatic-awk

A CLI phylomatic written in Awk

Phylomatic is a tool for attaching members of a user-supplied list of taxa (in the ‘taxa’ file) to a master, or ‘mega’ phylogeny (in the ‘phylo’ file) at as terminal a position as possible, using the internal node names of the megatree.

Please see Webb and Donoghue (2005) for more information on the goals of the tool, and this page for a short history of its implementation.

Usage

Basic usage is:

phylomatic OPTIONS --newick <phylo_file> --taxa <taxa_file>

where OPTIONS are:

  • --noclean: Do not clean single-daughter nodes from output phylogeny
  • --fyout: Output a tabular fy representation of the output phylogeny

and required arguments are:

  • --newick <phylo_file>: a file containing a single Newick serialization of a phylogeny. Two key requirements: The taxon names must begin with a character from A-Z or a-z or _ (i.e. not numbers), and any branch lengths must not be in scientific notation (i.e. ‘0.0001’, not ‘1.0E-4’).
  • --taxa <taxa_file>: a file containing taxa to be grafted into the phylogeny. Format: plain text, one taxon per line. Parent taxa may be prefixed to the taxon to be matched with slashes (/); if the taxon name itself is not found in the phylogeny, one of its parent taxa may be. See below, and examples.

For example, to use the Zanne 2014 megatree included in the data/ directory, with an example list of taxa, in the examples/ directory, and send the Newick output to a file out.new:

phylomatic --newick data/zanne2014.new --taxa examples/taxa2 > out.new

The program may also be used to just convert a Newick file into fy format:

phylomatic --new2fy --newick <phylo_file>

Installation

The Awk script is self contained and can easily be run in any environment where GNU Awk is available.

Linux

Gawk is usually the default Awk on Linux, and usually comes pre-installed. The script can be run either as an executable using the hashbang on the first line #!/usr/bin/gawk:

./phylomatic

or explicitly as a script via:

gawk -f phylomatic --newick ...etc

Mac

The default Awk on Macs is not Gawk, but the script may run as is (though it uses Gawk extensions that are not POSIX standard). Run the script in a Terminal window with:

awk -f phylomatic --newick ...etc

If the script fails with syntax error or illegal statement errors, you will need to install Gawk, e.g., using Homebrew or Fink.

Windows

The script can be easily run using Gawk cross-compiled for Windows, and the CMD.EXE command prompt:

  • Download Gawk from Ezwinports and unzip on the Desktop.
  • (This step may not be needed... try gawk.exe first without it. Otherwise: download libgcc-6.3.0-1-mingw32-dll-1.tar.xz here. Then extract the file it contains: libgcc_s_dw2-1.dll and place this DLL file in the same directory as gawk.exe.)
  • Download the latest phylomatic-awk release, and unzip on the Desktop.
  • In the menubar search box, type CMD.EXE and open it. This is the old DOS commandline. MS Powershell can also be used.

Type these commands (altering the version numbers if different). The latest CMD.EXE has command line TAB-completion which speeds things up. Basic commands: dir = view directory files, cd = change directory, copy, more = see file contents.

cd Desktop\phylomatic-awk-1.0.0
dir
  ...
..\gawk-5.1.0-w32-bin\bin\gawk.exe -f phylomatic
..\gawk-5.1.0-w32-bin\bin\gawk.exe -f phylomatic --clean --newick data/zanne2014.new --taxa examples/taxa2
..\gawk-5.1.0-w32-bin\bin\gawk.exe -f phylomatic --clean --newick data/zanne2014.new --taxa examples/taxa2 > out.new
dir
  ...
more out.new

The taxa file

Each [RETURN]-delimited line of the file lists a set of hierarchical taxon names (delimited by ‘/’), which will be sought for as either terminal or internal node names in the megatree. An example:

  annonaceae/annona/Annona_cherimola
  annonaceae/annona/Annona_muricata
  fagaceae/Quercus_robur
  dipterocarpaceae/shorea/Shorea_parvifolia

The last name on each line is the name that will be spliced into the returned tree. Note that phylomatic will not match a taxon Z in x/y/Z where Z is an internal node in the megatree (reference) phylogeny. In the case where, for instance, an output tree of just genera is desired, but some of the genera appear in the megatree as internal node names, ‘dummy species’ names can be used genus (e.g., betulaceae/alnus/alnus_sp); a text editor can later be used to remove the ‘_sp’ from the output tree.

This ‘/’-delimited format allows the creation of unlimited user-defined phylogenetic structure. The program reads the string from right to left, matching the taxon at the first position it can in i) the ‘megatree,’ or ii) the growing user-defined tree. Hence, a taxa file containing:

annonaceae/g1/s1
annonaceae/g2/s2
annonaceae/g2/s3
annonaceae/g2/s4/ssp1
annonaceae/g2/s4/ssp2

will produce a tree containing: ((s1)g1,(s2,s3,(ssp1,ssp2)s4)g2)annonaceae. See taxa files the examples directory.