Publications

Web-Based Applications

• PipMaker and MultiPipMaker   [PipMaker publication]  [MultiPipMaker publication]
• PipHelper
           Retrieve data from the UCSC Genome Browser in a format suitable for
           further processing by PipMaker and MultiPipMaker.
• zPicture   [publication]
• EnteriX   [publication]
• GALA: Genome Alignment and Annotation Database   [publication]
• dbERGE II: Database of Experimental Results on Gene Expression
• PhenCode
           Connects phenotype and clinical data in locus-specific databases
           with the UCSC Genome Browser.
• HbVar database   [publication]
           A relational database of Hb variants and thalassemias, initially derived
           from Prof. Huisman's Syllabi (see next links) and regularly updated.
• A Syllabus of Human Hemoglobin Variants (1996)
• Most of  A Syllabus of Thalassemia Mutations (1997)

Software

• Reconstructing contiguous regions of an ancestral genome
• PipMaker and MultiPipMaker server software  (bzipped tar file of source code; beta version; latest release: 2011-Aug-12)
• LASTZ alignment program  (latest release: 1.04.03, 2019-Nov-14)
• [↑] BLASTZ alignment program  (obsolete; replaced by LASTZ)  (gzipped tar file of source code; latest release: 2004-Dec-22)   [publication]
• Documentation for the LAV alignment format (output from BLASTZ)
• Multiz and TBA alignment programs  (gzipped tar file of source code; latest release: 2009-Jan-21)   [publication]   [documentation]
• MultiPipMaker's alignment program  (gzipped tar file of source code; latest release: 2004-Dec-20)
• Simulation code for generating multi-alignment test data  (gzipped tar file of source code; latest release: 2004-Nov-20)
• Code to compare multi-alignments (one may be the simulated "true alignment")  (gzipped tar file of source code; latest release: 2004-Nov-20)
• Mathieu Blanchette's data and code for testing multiple aligners  (gzipped tar file; 15 M bytes; latest release: 2004-Feb-1)
• Tools For Use With PipMaker and MultiPipMaker   [PipTools publication]   [MultiPipTools publication]
• Gmaj interactive viewer for multiple alignments  latest release: 2008-Jun-30
• Laj interactive viewer for pairwise alignments  latest release: 2005-Dec-14
• Sim4 alignment program  revised 2012-Oct-10   [instructions]   [publication]
• Five tools for finding conserved regions in multiple alignments   [publication]
• Tools for post-processing long pairwise alignments   [publication]
• lav2axt
• HomologMiner
• ModelFinder  (zipped file of source code; latest release: 2008-Aug-21)
• Phylogenomic tools  (gzipped tar file of source code; latest release: 2007-Feb-23)
• VennGenerator  (latest release: 2009-Jul-23)
• DIAL  (gzipped tar file of source code; latest release: 2011-Jun-06)
• YASRA  (gzipped tar file of source code; latest release: 2014-Mar-27)
• 3SEQ_2D  (gzipped tar file; 6 M bytes; latest release: 2010-Aug-30)   [publication]
• CHAP  (fast version; gzipped tar file; 71 Mb; 2011-Aug-02)
  CHAP  (compact version; gzipped tar file; 2.4 Mb; 2011-Aug-02)
• CHAP 2  (link to GitHub)
• Other software

Tutorials

• Phenotype Association Tools in Galaxy

Examples

• Pairwise alignment examples for specific loci
• Annotated images of multiple alignments: HSs in the mammalian beta-globin LCR

How to contact us

NOTE:  These pages are under constant revision, and are located on several physical systems. Please be careful to only bookmark our published URL, http://www.bx.psu.edu/, otherwise your links to internal pages may go stale.

$Revision: 1.105 $$Date: 2019/11/14 22:59:17 $