Title: Software  
Author: Craig Michael Dupree Aug 07, 2009
Last Changed by: Ming Cheng Nov 19, 2013
Tiny Link: (useful for email) https://wikis.utexas.edu/x/hRBp
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Incoming Links
The Center for Computational Biology and Bioinformatics (6)
    Page: Secure Shell
    Page: Documentation
    Page: Cluster Specific Documentation
    Page: UNIX Notes
    Home page: Home
    Page: New Users Guide
Hierarchy
Parent Page
    Home page: Home
Children (11)
    Page: Bioperl
    Page: Consed/Phred/Phrap
    Page: ICS
    Page: IM/IMA
    Page: install-consed
    Page: install-phrap
    Page: install-phred
    Page: python-intro
    Page: R-intro
    Page: rRNAScan
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Recent Changes
Time Editor  
Nov 19, 2013 11:02 Ming Cheng View Changes
Migrated to Confluence 5.3
Nov 19, 2013 11:02 Ming Cheng View Changes
Nov 19, 2013 11:01 Ming Cheng View Changes
Nov 19, 2013 11:00 Ming Cheng View Changes
Nov 19, 2013 10:57 Ming Cheng  
Outgoing Links
External Links (21)
    ai.eecs.umich.edu/people/dreeves/mash/
    wikis.utexas.edu/display/CCBB/python-intro
    www.utexas.edu/its/bevoware
    https://wikis.utexas.edu/display/CCBB/rRNAScan
    www.netlib.org/blas/
    https://wikis.utexas.edu/display/bioiteam/SOAPtrans
    qiime.org/
    biopython.org/wiki/Main_Page
    math-atlas.sourceforge.net/
    computerstore.utexas.edu
    https://wikis.utexas.edu/pages/viewpage.action?pageId=54009…
    icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php …
    https://wikis.utexas.edu/display/CCBB/ICS
    icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php …
    www.utexas.edu/its/sds
    www.affymetrix.com/partners_programs/programs/developer/too…
    wikis.utexas.edu/display/CCBB/Bioperl
    www.netlib.org/lapack/
    https://www.ph.utexas.edu/software/
    wikis.utexas.edu/display/CCBB/R-intro
    beast.bio.ed.ac.uk/Main_Page
Bioinformatics Team (BioITeam) at the University of Texas (51)     Page: Hmmer
    Page: Removing duplicates from alignment output
    Page: IGV
    Page: Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts
    Page: BioMart Perl APIs
    Page: Trinity
    Page: Velvet
    Page: Data compression programs
    Page: SHRiMP
    Page: BWA
    Page: muscle
    Page: ssh - generating keys
    Page: GMAP and GSNAP
    Page: Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts
    Page: Fastx Toolkit
    Page: MeV
    Page: MaqView
    Page: Phred, Phrap, Consed, cross_match, daev
    Page: Breakdancer
    Page: SAMStat
    Page: Blast
    Page: SOAP
    Page: GeneWise
    Page: GS Reference mapper
    Page: Clustering programs - MCL and usearch, uclust
    Page: Circos
    Page: GS Run processor and run browser
    Page: Picard
    Page: Get FASTQ Format
    Page: BLAST tools
    Page: Annovar
    Page: Geneid
    Page: Bowtie
    Page: MAQ
    Page: Tophat- Cufflinks
    Page: ABI's SOLiD de novo pipeline
    Page: FastQC
    Page: Sff file manipulation tools
    Page: Genome Analysis Tool Kit
    Page: mapreads
    Page: glimmer3
    Page: GS De novo assembler
    Page: Bioconductor
    Page: SAMTOOLS
    Page: GS Amplicon variant analyzer
    Page: Mosaik
    Page: BFAST
    Page: Small RNA Pipeline
    Page: ABYSS
    Page: BOOST libraries
    Page: MIRA
The Center for Computational Biology and Bioinformatics (4)     Page: Software
    Page: SATE_INSTRUCTIONS
    Page: Hardware
    Page: Environmental Modules