phyloRAD

A package reconstructs phylogeny from RADseq data using alignment and assembly-free (AAF) method.

Citation: Reconstructing phylogeny from reduced‐representation genome sequencing data without assembly or alignment, Huan Fan, Anthony R Ives, Yann Surget‐Groba, June 2018, Molecular Ecology Resources DOI: 10.1111/1755-0998.12921, Full text

This package includes executables from Phylokmer (Author: Jue Ruan), PHYLIP (Author: Joe Felsenstein) and ReadsSelector (Author: Chengxi Ye).

Requirements

• UNIX system (Linux or macOS)
• g++/gcc compilers
• Python 2.7+ or higher (including 3.x)

Note that only v1.0 supports both python2.7 and python 3.x. v1.1+ only supports python3.5 and 3.6.

Installation:

Warning: the new version (where gzip files are taken) is only tested on linux.

1. Download or clone this repo.
2. Install a c++ library called gzstream so that ReadsSelector could process gzipped files.
   i. cd into the subdirectory source
   ii. tar xzvf gzstream.tgz
   iii. cd gzstream iv. Run make
   v. Run export CPLUS_INCLUDE_PATH=PATH_TO_phyRAD/source/gzstream
   vi. Run export LIBRARY_PATH=PATH_TO_phyRAD/source/gzstream
3. cd ../ out into source, run make all and make clean
4. cp the executables you just compiled to your PATH or working directory, including consense, treedist, fitch_kmerX, fitch_kmerX_long, kmer_count(x), kmer_merge and ReadsSelector.
5. Make sure python knows where the AAF module is. You can achive this by
   • Put the AAF.py in your working directory
   • Add where AAF.py is to your PATH export PATH=/PATH/TO/AAF.py:$PATH
   • Put AAF.py in your site-packages folder. If you don't know where your site-packages folder is, try: >>> import site; site.getsitepackages()

Usage and Examples:

Input: Fasta or fastq files. If there are multiple files for one sample, put them in one folder.
Output: Newick format phylogenetic tree.

Using shared-by-all reads selection::

$ phyloRAD_sba.py -h

Usage: phyloRAD_sba.py [options]

Options:
  --version    show program's version number and exit
  -h, --help   show this help message and exit
  -k KLEN      k for reconstruction, default = 25
  --ks=KSLEN   k for reads selection, default = 25
  -n FILTER    k-mer filtering threshold, default = 1
  -d DATADIR   directory containing the data, default = data/
  -G MEMSIZE   total memory limit (in GB), default = 4
  -t NTHREADS  number of threads to use, default = 1
  -l           use fitch_kmerX_long instead of fitch_kmerX

Example:

 $ phyloRAD_sba.py -d test_data -G 4 -t 2 -k 15 --ks 15 -n 2

Using pairwise reads selection::

$ phyloRAD_pairwise.py -h
Usage: phyloRAD_pairwise.py [options]

Options:
  --version    show program's version number and exit
  -h, --help   show this help message and exit
  -k KLEN      k for reconstruction, default = 25
  --ks=KSLEN   k for reads selection, default = 25
  -n FILTER    k-mer filtering threshold, default = 1
  -d DATADIR   directory containing the data, default = data/
  -G MEMSIZE   total memory limit (in GB), default = 4
  -t NTHREADS  number of threads to use, default = 1
  -l           use fitch_kmerX_long instead of fitch_kmerX

Examples:

$ phyloRAD_pairwise.py -d test_data -G 4 -t 2 -k 15 --ks 15 -n 2