Welcome to the MaxBin download page.

MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page.

Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin after the binning process is finished.


For instructions on how to run MaxBin, please read the README and look at the FAQ.

MaxBin is released under the BSD license.

MaxBin can also be downloaded from Sourceforge!

The MaxBin manuscript has been accepted for publication by the journal Microbiome.
See below for the MaxBin manuscript supporting materials.


Current Version

NEW! MaxBin 1.3 (5/12/2014)
  • Fixed bugs relating having 100+ bins.
  • Cleaned up the log file.
  • Added the -max_iteration option to adjust the maximum number of EM runs (default 50).
  • Unclassified sequences and sequences shorter than minimum length threshold are now stored in different files (.tooshort and .noclass).

Older Versions

MaxBin 1.2.1 (3/14/2014)
  • Added support for the FASTQ format when the -reads option is specified.

MaxBin 1.2 (1/27/2014)
  • Stabalized the connection between MaxBin and auxiliary software packages.
  • Added the function to check the output of auxiliary software packages. MaxBin will now output warning messages and stop running when there are errors.
  • Bug fixes.

MaxBin 1.1 (10/15/2013)
  • Fixed the bug that crashes the program when a FASTA file with a long single line is encountered.
  • Implemented recursive binning, in which binned FASTA files will be checked separately for further binning possibilities.
  • Make the summary file more informative by adding Completeness (i.e. how complete the binned genomes are), Genome sizes and GC content.
  • Sort the bins by descending order of their abundance levels.
  • Add total number of marker genes and the number of unique marker genes into 2nd and 3rd column of the .marker file.
  • Add a function to automatically "switch" to more powerful binning mode once MaxBin finds that it cannot find enough marker genes to determine bin number.

MaxBin 1.0.1 (6/25/2013)
  • Added -min_contig_len parameter for users to decide the minimum contig length acceptable in MaxBin. Default value of minimum contig length is 1000.
  • Added -plotmarker option and integrated it with R (Rscript) to plot the marker gene heatmap as PDF file.
  • Added -verbose option for debug usage.
  • Fix bug when the coverage of certain contig is 0. This should not happen very often, but codes are added to avoid program crash on such circumstance.

MaxBin 1.0 (not available for download) (4/29/2013)
  • Integrated core MaxBin algorithm into perl script to connect with 3rd-party software.
  • Added compile_MaxBin script for users to compile MaxBin core program and all 3rd-party software.


MaxBin Manuscript Supporting Materials



MaxBin FAQ

Q: How do I compile MaxBin from scratch?
A: Please run "./compile_MaxBin" to build the core program. You also need to download and install auxiliary software packages, including Bowtie2, FragGeneScan, and HMMER3 to run MaxBin correctly.

Q: I already have my own auxiliary software packages installed in my computer. Do I need to install them again?
A: Technically you don't need to install the software packages again; however, if your software packages are older than that used in MaxBin test, we recommend you update or download and install new software packages again. This will ensure MaxBin running process is free of errors.

Q: I don't have abundance information for my assembled scaffolds. What can I do?
A: MaxBin can find the abundance information from the sequencing reads automatically. Simply provide your reads file (in either FASTQ or FASTA format) using the -reads option. Currently MaxBin can only deal with one reads file at a time. Please concatenate your reads files if you have more than one of them.

Q: I ran MaxBin with -reads option. Where can I find the scaffold abundance information that MaxBin generated for me?
A: The abundance information is stored at (output file header).abund. You can use this file for re-run MaxBin for any other purpose.

Q: I have a question about MaxBin. Who should I contact?
A: Please contact the developer Yu-Wei Wu at ywwei@lbl.gov.