Accurate Species TRee Reconstruction with Internode Distances
Python C++ CMake
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README.md

ASTRID 1.4

Download HERE

Accurate Species TRee Reconstruction with Internode Distances

For more information, see http://pranjalv123.github.io/ASTRID/

Join the ASTRID user group at https://groups.google.com/forum/#!forum/astrid-users/

Installation (binary)

ASTRID is available for Linux, Mac OS X, and Windows.

Download the appropriate binary file for your operating system at https://github.com/pranjalv123/ASTRID/releases

You may need to run

chmod +x ASTRID-osx 

in order to be able to execute it.

Also, you can either do

mv ASTRID-osx ASTRID

or use ASTRID-osx when ASTRID is specified in the documentation. (replacing ASTRID-osx with ASTRID-linux on linux)

Installation (source)

YOU DO NOT NEED TO DO ANY OF THIS TO RUN ASTRID - THIS IS PRIMARILY FOR ASTRID DEVELOPERS

Dependencies:

Clone the repository and enter the directory.

  git clone git@github.com:pranjalv123/ASTRID.git
  cd ASTRID

Create a build folder

  mkdir build && cd build

Configure and build

  cmake ../src/
  make

Make will automatically download and compile FastME 2, and place all necessary files in build/bin/.

Packaging

Get PyInstaller (http://www.pyinstaller.org/), and run pyinstaller ASTRID.spec from the repository root. This will produce the dist folder and an ASTRID executable in it.

Usage

  ASTRID [-h] -i INPUT [-b --bsfile BSFILE]
         [--bslist BSLIST [BSLIST ...]] [-r --bsreps BSREPS] [-o OUTPUT]
         [-m METHOD] [-c CACHE] [--taxon-cutoff TAXON_CUTOFF]

  ASTRID: Accurate Species TRees from Internode Distances.

  optional arguments:
-h, --help            show this help message and exit
-i INPUT, --input INPUT
		      File containing gene trees as newick strings
-b --bsfile BSFILE    File containing a list of bootstrap replicate files,
		      one file per gene
--bslist BSLIST [BSLIST ...]
		      List of bootstrap files
-r --bsreps BSREPS    Number of bootstrap replicates
-o OUTPUT, --output OUTPUT
		      Output file for species tree
-m METHOD, --method METHOD
		      Distance-based method to use (default: fastme if the
		      distance matrix is complete, bionj otherwise
-c CACHE, --cache CACHE
		      Save distance matrix in PHYLIP format, or use cached
		      matrix if it exists (useful for trying multiple
		      distance-based methods)
--taxon-cutoff TAXON_CUTOFF
		      Only take trees with at least this many taxa

ASTRID is also easy to use from within Python:

import dendropy
import ASTRID
tl = dendropy.TreeList.get_from_path('test/song_mammals.424.gene.tre', 'newick')
a = ASTRID.ASTRID(tl)
a.run('auto')
print str(a.tree)