MacQIIME Deprecated & No-Longer Needed!

Since the QIIME pipeline was updated to version 2.0, MacQIIME is now outdated and is no-longer needed! Thanks to the QIIME developers, QIIME 2.x will now install on a Mac using the built-in automated installation via miniconda. For more information and installation instructions, check out!  If you're used to the MacQIIME 1.x command-line interface, I'd suggest following the q2cli > Installing QIIME 2 > Native Installation instructions on You are still welcome to install MacQIIME if you like, but note that it is the old 1.9.1 version of QIIME from 2015.

It is also possible to have MacQIIME 1.9.1 and QIIME 2 installed at the same time, if you really want to. They shouldn't fight with each other, as long as you only have one of them sourced at any given time.

Old MacQIIME 1.9.1 on Mac OS X

MacQIIME 1.9.1 20150604 OS10.7
OS 10.7+ | QIIME 1.9.1 | June 4th, 2015
Download   [ MD5 6634cb226d71ecf17d60483e6039f66a ]

Save the file (don't open it with the Archive Unitility) and follow the install instructions. The above package will only work on Mac OS X versions 10.7 and up. I've tested it on OS 10.10 (on an old MacBook Pro), 10.7 (on a Mini) and 10.9 (on one of those fancy new black cylinder-shaped Mac Pros that look like an air purifier). Sorry I couldn't continue to support OS 10.6; as of MacQIIME 1.9.1 the system requirement is now to have OS 10.7 or higher. This was in part due to an upgrade to Anaconda Python, but Anaconda's 10.7 pre-req is directly related to the compatibility problems that I was facing anyway.

Citing QIIME.  The MacQIIME package includes many separate software packages developed by many different research groups, all wrapped together by the QIIME scripts. Since you install MacQIIME in just one step, all those separate software packages seem somewhat invisible, and you may not even notice whose software you're really using. Here is a guide to some important references you may want to cite.


An easy way to use QIIME on Mac OS X

MacQIIME is a precompiled installation of QIIME, with all its dependencies, placed in one easy-to-install and easy-to-update folder. It will install (and can be quickly deleted, if you like) in Mac OS 10.6 and up. It will not replace, modify or break any existing software on your computer. MacQIIME is normally invisible to your terminal shell until you source the environment variables with "macqiime" command, in order to keep things in a neat bottle and avoid compatibility issues with other software.

In a collaboration with multiple labs on high-throughput sequencing analysis, we needed an easy way to install QIIME (and its many dependencies) and keep it updated on many Mac computers. This self-contained MacQIIME package seemed like a nice solution. I'm making MacQIIME available as a public download so that others might benefit from the initial bit of work that went into it. I'm not a software developer, though I know my way around Unix, and I use QIIME quite frequently. That said, this open-source package is provided free with no warantee, no formal support, and no guarantee that it will or will not do anything.

Citing QIIME.  The QIIME source code was developed by the Knight Lab and others. Since MacQIIME includes this as well as many other software packages, here is a guide to some common references you may want to cite.

If you have any questions or comments about MacQIIME, please feel free to contact Jeff Werner.

Installing MacQIIME

Main page: MacQIIME Installation

The MacQIIME package will install only on Intel Mac computers with OS X 10.7 and up. The tgz file (download link on top of this page) includes an installation script, which you will have to use from the command line. You will be asked for an sudo password, so you must have administrative privilages and access to the root (/) of the filesystem to install. This was necessary because a number of packages require absolute references to directory locations.

For more details on the install process, please see MacQIIME Installation.

Other Options for Trying Out QIIME

The easiest way to try out QIIME is with the QIIME Virtual Box. This will work on any OS (Windows, Mac, Linux, etc) as long as the computer has two or more cores. I've used this virtual box to teach students how to process high-throughput 16S rRNA gene sequences, and all the students were able to quickly install it and start analyzing data. The MacQIIME package, however, may be useful to someone who wants to use QIIME more extensively in Mac OS X. As a native installation, it has more memory and CPU resources available, and direct access to the base filesystem.

Of-course, the best way to implement QIIME is to compile and install everything yourself. The installation is a solid day worth of work, but the things you will learn are very helpful in understanding how everything works. :)

What is Included in MacQIIME?

  • QIIME (current stable release, 1.9.1)
  • A custom install of Anaconda Python 2.7.10, with numpy, matplotlib, and PyCogent; This python install will be invisible to your system until you open a nes subshell with the "macqiime" command.
  • mothur
  • UCLUST (special version for QIIME only -- I highly recommend trying out the regular version of USEARCH for other high-throughput searching and clustering)
  • ChimeraSlayer
  • PyNAST
  • FastTree
  • RDP Classifier
  • Infernal
  • And more! (tax2tree, pplacer, cd-hit, muscle, clearcut, raxml...)

Not included, but may be needed: You'll probably have to install or update XQuartz; Legacy NCBI blast is not installed (assuming many people have their own install of this); AmpliconNoise is not installed (it requires custom compilation, dependent on MPI, specific to your system); USEARCH is not installed, due to licensing; R and associated functions are not installed.