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Software for motif discovery and next generation sequencing analysis

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Hardware Requirements (recommended): 2+ Gb memory (4-8+ Gb), 10+ Gb Hard Drive space (50+ Gb)
Software Requirements: Unix compatible OS (or cygwin), perl, gcc, make, wget (optional for full functionality: R, DESeq2, blat, bedGraphToBigWig, liftOver)
License: GPLv3

HOMER works on pretty much any Linux/UNIX systems, including MacOS (if Xcode compilers are installed) and on Windows using either cygwin or a Linux subsystem.

If you are looking specifically for HOMER2, you are in the right place! HOMER2 is integrated into HOMER.

Full Program Download

Alabtkar Fy Laj Amrad Aldhkwrt- Ttwrat Jdydt Fy... Apr 2026

Al-maradh al-dhkwrt, au al-sukkar, huwa maradh shay’ li-kathirin min al-nas fi al-‘alam. Huwa yusabbab bi-takhalluf fi al-insulin, hormone muhim li-taswiyat mustawayat al-sukkar fi al-dam. Al-dhkwrt yusabbab bi-kathira min al-amrad, wa huwa yata’aththar ‘ala al-qalb, al-kily, al-‘ayn, wa al-as’ab.

Al-mustaqbal li-al-abtkar fy laj amrad al-dhkwrt huwa mustaqbal wajid. Al-ba’hthun yastakhdimun al-tiknulujya al-jadida li-tatwir ‘ilaj jadid li-al-dhkwrt. Al-tathirat al-jadida fi al-abtkar fy laj amrad al-dhkwrt tata’aththar bi-kathira min al-fawa’id, wa hiya tus’takhdam li-taswiyat mustawayat al-sukkar fi al-dam, wa taqall al-khatar al-muta’alliq bi-al-dhkwrt. alabtkar fy laj amrad aldhkwrt- ttwrat jdydt fy...

Fi al-akhira, kana huna tathirat jadida fi al-abtkar fy laj amrad al-dhkwrt. Al-ba’hthun yastakhdimun al-tiknulujya al-jadida li-tatwir ‘ilaj jadid li-al-dhkwrt. Al-tathirat al-jadida hiya: huwa maradh shay&rsquo

Program Components and Older Versions

homer2 program - key executable for HOMER motif discovery (homerCppOnly.*.zip). (This archive actually contains all of the c++ executable, not just homer2). Unzip in the desired directory and simply type "make" to compile the program.

The configuration script really doesn't deal with older versions, but you can download older versions yourself should you really feel like using inferior data or software!

Old Versions of HOMER Software
Old Versions of Organism Packages
Old Versions of Promoter Packages
Old Versions of Genome Packages

Update Information

Change Log - Short description of recent changes

update.txt - Current HOMER configuration list (Currently support human hg17/hg18/hg19, mouse mm8/mm9, rat rn4, X. tropicalis xenTro2, drosophila dm3, and C. elegans ce6, Zebrafish danRer7, yeast sacCer2, Arabidopsis tair10, Rice msu6, Pombe ASM294v1)

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Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu