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BLAST
Cister
ClustalW
ClustalX
Comet
Dotter
FASTA
fastDNAml
GeneMachine
GENSCAN
HMMer
HMMgene
MrBayes
MZEF
PHRED/PHRAP/Consed
PHYLIP
ReadSeq
RepeatMasker
SEG
sim4
Sputnik
Treetool
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BLAST
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National Center for Biotechnology Information
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BLAST is the Basic Local Alignment Search Tool. It is a set of search programs designed to explore all available sequence databases in either protein or DNA. This software has been designed to achieve great speeds while keeping a well-defined statistical interpretation.
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BLAST is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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Hammer
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2.2.15
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http://gears.aset.psu.edu/hpc/software/bioinf/blast
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09-Nov-2006
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LION-XB
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2.2.15
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http://gears.aset.psu.edu/hpc/software/bioinf/blast
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09-Nov-2006
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LION-XC
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2.2.15
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http://gears.aset.psu.edu/hpc/software/bioinf/blast
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29-May-2007
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LION-XL
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2.2.8
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http://gears.aset.psu.edu/hpc/software/bioinf/blast
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07-Oct-2004
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LION-XM
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2.2.8
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http://gears.aset.psu.edu/hpc/software/bioinf/blast
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03-Nov-2004
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LION-XO
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2.2.15
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http://gears.aset.psu.edu/hpc/software/bioinf/blast
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09-Nov-2006
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Unisys
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2.2.11
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http://gears.aset.psu.edu/hpc/software/bioinf/blast
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02-Apr-2007
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Versions listed in bold are the default version.
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Cister
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Martin Frith
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Cister predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.
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Cister is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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Hammer
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/cister
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09-Nov-2006
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LION-XB
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/cister
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09-Nov-2006
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LION-XC
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/cister
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29-May-2007
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LION-XL
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/cister
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07-Oct-2004
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LION-XM
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/cister
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09-Nov-2006
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LION-XO
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/cister
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09-Nov-2006
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Versions listed in bold are the default version.
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ClustalW
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Institut de Genetique et de Biologie Moleculaire et Cellulaire
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ClustalW is a general purpose multiple alignment program for DNA or proteins.
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ClustalW is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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1.82
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http://gears.aset.psu.edu/hpc/software/bioinf/clustalw
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07-Oct-2004
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LION-XM
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1.82
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http://gears.aset.psu.edu/hpc/software/bioinf/clustalw
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03-Nov-2004
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Versions listed in bold are the default version.
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ClustalX
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Institut de Genetique et de Biologie Moleculaire et Cellulaire
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Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display.
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ClustalX is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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1.81
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http://gears.aset.psu.edu/hpc/software/bioinf/clustalx
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07-Oct-2004
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LION-XM
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1.81
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http://gears.aset.psu.edu/hpc/software/bioinf/clustalx
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03-Nov-2004
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Versions listed in bold are the default version.
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Comet
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Martin Frith
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Comet finds statistically significant clusters of cis-element motifs in a DNA sequence.
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Comet is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/comet
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07-Oct-2004
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LION-XM
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/comet
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03-Nov-2004
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Versions listed in bold are the default version.
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Dotter
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Karolinska Institutet Center for Genomics Research
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Dotter is a graphical dotplot program for detailed comparison of two sequences.
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Dotter is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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3.0
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http://gears.aset.psu.edu/hpc/software/bioinf/dotter
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07-Oct-2004
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LION-XM
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3.0
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http://gears.aset.psu.edu/hpc/software/bioinf/dotter
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03-Nov-2004
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Versions listed in bold are the default version.
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FASTA
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National Center for Biotechnology Information
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No product description available.
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FASTA is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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3.4t10
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http://gears.aset.psu.edu/hpc/software/bioinf/fasta
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07-Oct-2004
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LION-XM
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3.4t10
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http://gears.aset.psu.edu/hpc/software/bioinf/fasta
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03-Nov-2004
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Versions listed in bold are the default version.
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fastDNAml
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Ribosomal Database Project
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fastDNAml is an attempt to solve the same problem as DNAML (part of the PHYLIP package), but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable.
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fastDNAml is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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3.3
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http://gears.aset.psu.edu/hpc/software/bioinf/fastdnaml
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07-Oct-2004
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LION-XM
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3.3
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http://gears.aset.psu.edu/hpc/software/bioinf/fastdnaml
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03-Nov-2004
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Versions listed in bold are the default version.
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GeneMachine
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National Human Genome Research Institute
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GeneMachine is an integrated tool intended to perform both comparative and predictive gene identification techniques in a single run.
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GeneM is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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0.23
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http://gears.aset.psu.edu/hpc/software/bioinf/genem
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07-Oct-2004
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LION-XM
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0.23
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http://gears.aset.psu.edu/hpc/software/bioinf/genem
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03-Nov-2004
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Versions listed in bold are the default version.
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GENSCAN
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Christopher Burge
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GENSCAN is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants.
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GENSCAN is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/genscan
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20-Feb-2007
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LION-XM
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/genscan
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20-Feb-2007
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Versions listed in bold are the default version.
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HMMer
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Washington University in St. Louis
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Used to profile hidden Markov models.
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HMMer is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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2.2g
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http://gears.aset.psu.edu/hpc/software/bioinf/hmmer
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07-Oct-2004
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LION-XM
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2.2g
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http://gears.aset.psu.edu/hpc/software/bioinf/hmmer
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03-Nov-2004
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Versions listed in bold are the default version.
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HMMgene
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Center for Biological Sequence Analysis
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HMMgene is a program for prediction of genes in anonymous DNA.
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HMMgene is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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1.1e
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http://gears.aset.psu.edu/hpc/software/bioinf/hmmgene
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07-Oct-2004
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LION-XM
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1.1e
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http://gears.aset.psu.edu/hpc/software/bioinf/hmmgene
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03-Nov-2004
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Versions listed in bold are the default version.
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MrBayes
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John P. Huelsenbeck and Fredrik Ronquist
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MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.
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MrBayes is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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2.01
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http://gears.aset.psu.edu/hpc/software/bioinf/mrbayes
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07-Oct-2004
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LION-XM
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2.01
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http://gears.aset.psu.edu/hpc/software/bioinf/mrbayes
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03-Nov-2004
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Versions listed in bold are the default version.
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MZEF
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Cold Spring Harbor Laboratory
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MZEF predicts internal coding exons in genomic DNA sequences. It allows users to predict putative internal protein coding exons, adjust prior probability and to output alternative overlapping exons.
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MZEF is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/mzef
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07-Oct-2004
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LION-XM
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/mzef
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03-Nov-2004
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Versions listed in bold are the default version.
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PHRED/PHRAP/Consed
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Phil Green
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PHRED/PHRAP/Consed | This software reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
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PhPhC is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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0.000925.c
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No on-line instructions available
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07-Oct-2004
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LION-XM
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0.000925.c
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No on-line instructions available
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03-Nov-2004
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Versions listed in bold are the default version.
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PHYLIP
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University of Washington Dept. of Genome Sciences
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PHYLIP is a package of programs for inferring phylogenies.
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PHYLIP is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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3.5c
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http://gears.aset.psu.edu/hpc/software/bioinf/phylip
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07-Oct-2004
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LION-XM
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3.5c
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http://gears.aset.psu.edu/hpc/software/bioinf/phylip
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03-Nov-2004
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Versions listed in bold are the default version.
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ReadSeq
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Indiana University Dept. of Biology
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Converts input DNA/AA sequence to specified format.
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ReadSeq is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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2.1.7
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http://gears.aset.psu.edu/hpc/software/bioinf/readseq
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07-Oct-2004
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LION-XM
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2.1.7
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http://gears.aset.psu.edu/hpc/software/bioinf/readseq
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03-Nov-2004
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Versions listed in bold are the default version.
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RepeatMasker
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Genetic Information Research Institute
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Screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.
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repeatmasker is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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20020713
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http://gears.aset.psu.edu/hpc/software/bioinf/repeatmasker
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07-Oct-2004
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LION-XM
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20020713
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http://gears.aset.psu.edu/hpc/software/bioinf/repeatmasker
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03-Nov-2004
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Versions listed in bold are the default version.
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SEG
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National Center for Biotechnology Information
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SEG divides sequences into contrasting segments of low-complexity and high-complexity.
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SEG is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/seg
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07-Oct-2004
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LION-XM
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/seg
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03-Nov-2004
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Versions listed in bold are the default version.
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sim4
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Comp. Sci. and Engr. and Biochem. and Mol. Bio. at Penn State Univ.
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sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene.
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sim4 is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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20011012
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http://gears.aset.psu.edu/hpc/software/bioinf/sim4
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07-Oct-2004
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LION-XM
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20011012
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http://gears.aset.psu.edu/hpc/software/bioinf/sim4
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03-Nov-2004
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Versions listed in bold are the default version.
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Sputnik
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University of Washington Dept. of Molecular Biotechnology
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Sputnik is a C language program that searches DNA sequence files in Fasta format for microsatellite repeats. A sequence file is specified on the command line and the resulting hits are written to stdout along with their position in the sequence, length, and a score determined by the length of the repeat and the number of errors.
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Sputnik is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/sputnik
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07-Oct-2004
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LION-XM
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N/A
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http://gears.aset.psu.edu/hpc/software/bioinf/sputnik
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03-Nov-2004
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Versions listed in bold are the default version.
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Treetool
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Ribosomal Database Project
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Treetool is an interactive tool for displaying, editing, and printing phylogenetic trees.
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Treetool is available on the following HPC machines:
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Machine
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Version
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Instructions
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Last Update
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LION-XL
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2.0.2
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http://gears.aset.psu.edu/hpc/software/bioinf/treetool
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07-Oct-2004
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LION-XM
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2.0.2
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http://gears.aset.psu.edu/hpc/software/bioinf/treetool
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03-Nov-2004
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Versions listed in bold are the default version.
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