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Bioinformatics

Compilers and Programming Tools

Computational Chemistry

Finite Element Solvers

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Mathematics

Numerical Libraries

Optimization

Parallel Programming Libraries and Tools

Solid Modeling

Statistics

Bioinformatics


Ancestrymap
BLAST
Cister
ClustalW
ClustalX
Comet
Dotter
FASTA
fastDNAml
GeneMachine
GENSCAN
HMMer
HMMgene
MrBayes
MZEF
PHYLIP
ReadSeq
SEG
sim4
Sputnik
Treetool


Ancestrymap

The Broad Institute

The software estimates the ancestry along the genome of a sample population resulting from recent admixture between two ethnic groups. The program uses data from individuals genotyped at a set of markers, where the markers chosen are preferably the ones that differ significantly in frequency between the two ancestral populations.

ancestrymap is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

LION-XB

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

LION-XC

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

LION-XD

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

LION-XJ

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

LION-XO

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

Unisys

-

http://genepath.med.harvard.edu/~reich/contents.htm

17-Oct-2008

Versions listed in bold are the default version.


BLAST

National Center for Biotechnology Information

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.

BLAST is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

2.2.15

http://rcc.its.psu.edu/hpc/software/bioinf/blast

10-Sep-2008

LION-XB

2.2.15

http://rcc.its.psu.edu/hpc/software/bioinf/blast

10-Sep-2008

LION-XC

2.2.15

http://rcc.its.psu.edu/hpc/software/bioinf/blast

10-Sep-2008

LION-XD

2.2.15

http://rcc.its.psu.edu/hpc/software/bioinf/blast

16-Sep-2008

LION-XJ

2.2.15

http://rcc.its.psu.edu/hpc/software/bioinf/blast

10-Sep-2008

LION-XO

2.2.15

http://rcc.its.psu.edu/hpc/software/bioinf/blast

10-Sep-2008

Unisys

2.2.11

http://rcc.its.psu.edu/hpc/software/bioinf/blast

10-Sep-2008

Versions listed in bold are the default version.


Cister

Martin Frith

Cister predicts regulatory regions in DNA sequences by searching for clusters of cis-elements.

Cister is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

N/A

http://rcc.its.psu.edu/hpc/software/bioinf/cister

10-Sep-2008

LION-XB

N/A

http://rcc.its.psu.edu/hpc/software/bioinf/cister

10-Sep-2008

LION-XC

N/A

http://rcc.its.psu.edu/hpc/software/bioinf/cister

10-Sep-2008

LION-XD

N/A

http://rcc.its.psu.edu/hpc/software/bioinf/cister

22-Sep-2008

LION-XJ

N/A

http://rcc.its.psu.edu/hpc/software/bioinf/cister

10-Sep-2008

LION-XO

N/A

http://rcc.its.psu.edu/hpc/software/bioinf/cister

10-Sep-2008

Versions listed in bold are the default version.


ClustalW

Institut de Genetique et de Biologie Moleculaire et Cellulaire

ClustalW is a general purpose multiple alignment program for DNA or proteins.

ClustalW is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalw

16-Sep-2008

LION-XB

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalw

16-Sep-2008

LION-XC

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalw

16-Sep-2008

LION-XD

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalw

16-Sep-2008

LION-XJ

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalw

16-Sep-2008

LION-XO

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalw

16-Sep-2008

Versions listed in bold are the default version.


ClustalX

Institut de Genetique et de Biologie Moleculaire et Cellulaire

Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display.

ClustalX is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalx

16-Sep-2008

LION-XB

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalx

16-Sep-2008

LION-XC

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalx

16-Sep-2008

LION-XD

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalx

16-Sep-2008

LION-XJ

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalx

16-Sep-2008

LION-XO

1.83

http://rcc.its.psu.edu/hpc/software/bioinf/clustalx

16-Sep-2008

Versions listed in bold are the default version.


Comet

Martin Frith

Comet finds statistically significant clusters of cis-element motifs in a DNA sequence.

Comet is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

http://rcc.its.psu.edu/hpc/software/bioinf/comet

16-Sep-2008

LION-XB

http://rcc.its.psu.edu/hpc/software/bioinf/comet

16-Sep-2008

LION-XC

http://rcc.its.psu.edu/hpc/software/bioinf/comet

16-Sep-2008

LION-XD

http://rcc.its.psu.edu/hpc/software/bioinf/comet

16-Sep-2008

LION-XJ

http://rcc.its.psu.edu/hpc/software/bioinf/comet

16-Sep-2008

LION-XO

http://rcc.its.psu.edu/hpc/software/bioinf/comet

16-Sep-2008

Versions listed in bold are the default version.


Dotter

Karolinska Institutet Center for Genomics Research

Dotter is a graphical dotplot program for detailed comparison of two sequences.

Dotter is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

http://rcc.its.psu.edu/hpc/software/bioinf/dotter

16-Sep-2008

LION-XB

http://rcc.its.psu.edu/hpc/software/bioinf/dotter

16-Sep-2008

LION-XC

http://rcc.its.psu.edu/hpc/software/bioinf/dotter

16-Sep-2008

LION-XD

http://rcc.its.psu.edu/hpc/software/bioinf/dotter

16-Sep-2008

LION-XJ

http://rcc.its.psu.edu/hpc/software/bioinf/dotter

16-Sep-2008

LION-XO

http://rcc.its.psu.edu/hpc/software/bioinf/dotter

16-Sep-2008

Versions listed in bold are the default version.


FASTA

National Center for Biotechnology Information

No product description available.

FASTA is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

3.4t25d9

http://rcc.its.psu.edu/hpc/software/bioinf/fasta

16-Sep-2008

LION-XB

3.4t25d9

http://rcc.its.psu.edu/hpc/software/bioinf/fasta

16-Sep-2008

LION-XC

3.4t25d9

http://rcc.its.psu.edu/hpc/software/bioinf/fasta

16-Sep-2008

LION-XD

3.4t25d9

http://rcc.its.psu.edu/hpc/software/bioinf/fasta

16-Sep-2008

LION-XJ

3.4t25d9

http://rcc.its.psu.edu/hpc/software/bioinf/fasta

16-Sep-2008

LION-XO

3.4t25d9

http://rcc.its.psu.edu/hpc/software/bioinf/fasta

16-Sep-2008

Versions listed in bold are the default version.


fastDNAml

Ribosomal Database Project

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.

fastDNAml is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

1.2.2

http://rcc.its.psu.edu/hpc/software/bioinf/fastDNAml

16-Sep-2008

LION-XB

1.2.2

http://rcc.its.psu.edu/hpc/software/bioinf/fastDNAml

16-Sep-2008

LION-XC

1.2.2

http://rcc.its.psu.edu/hpc/software/bioinf/fastDNAml

16-Sep-2008

LION-XD

1.2.2

http://rcc.its.psu.edu/hpc/software/bioinf/fastDNAml

16-Sep-2008

LION-XJ

1.2.2

http://rcc.its.psu.edu/hpc/software/bioinf/fastDNAml

16-Sep-2008

LION-XO

1.2.2

http://rcc.its.psu.edu/hpc/software/bioinf/fastDNAml

16-Sep-2008

Versions listed in bold are the default version.


GeneMachine

National Human Genome Research Institute

GeneMachine is an integrated tool intended to perform both comparative and predictive gene identification techniques in a single run.

GeneM is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

0.23

http://rcc.its.psu.edu/hpc/software/bioinf/genemachine

16-Sep-2008

LION-XB

0.23

http://rcc.its.psu.edu/hpc/software/bioinf/genemachine

16-Sep-2008

LION-XC

0.23

http://rcc.its.psu.edu/hpc/software/bioinf/genemachine

16-Sep-2008

LION-XD

0.23

http://rcc.its.psu.edu/hpc/software/bioinf/genemachine

16-Sep-2008

LION-XJ

0.23

http://rcc.its.psu.edu/hpc/software/bioinf/genemachine

16-Sep-2008

LION-XO

0.23

http://rcc.its.psu.edu/hpc/software/bioinf/genemachine

16-Sep-2008

Versions listed in bold are the default version.


GENSCAN

Christopher Burge

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.

GENSCAN is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

http://rcc.its.psu.edu/hpc/software/bioinf/genscan

16-Sep-2008

LION-XB

http://rcc.its.psu.edu/hpc/software/bioinf/genscan

16-Sep-2008

LION-XC

http://rcc.its.psu.edu/hpc/software/bioinf/genscan

16-Sep-2008

LION-XD

http://rcc.its.psu.edu/hpc/software/bioinf/genscan

16-Sep-2008

LION-XJ

http://rcc.its.psu.edu/hpc/software/bioinf/genscan

16-Sep-2008

LION-XO

http://rcc.its.psu.edu/hpc/software/bioinf/genscan

16-Sep-2008

Versions listed in bold are the default version.


HMMer

Washington University in St. Louis

Used to profile hidden Markov models.

HMMer is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

2.3.2

http://rcc.its.psu.edu/hpc/software/bioinf/hmmer

16-Sep-2008

LION-XB

2.3.2

http://rcc.its.psu.edu/hpc/software/bioinf/hmmer

16-Sep-2008

LION-XC

2.3.2

http://rcc.its.psu.edu/hpc/software/bioinf/hmmer

16-Sep-2008

LION-XD

2.3.2

http://rcc.its.psu.edu/hpc/software/bioinf/hmmer

16-Sep-2008

LION-XJ

2.3.2

http://rcc.its.psu.edu/hpc/software/bioinf/hmmer

16-Sep-2008

LION-XO

2.3.2

http://rcc.its.psu.edu/hpc/software/bioinf/hmmer

16-Sep-2008

Versions listed in bold are the default version.


HMMgene

Center for Biological Sequence Analysis

HMMgene is a program for prediction of genes in anonymous DNA.

HMMgene is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

1.1

http://rcc.its.psu.edu/hpc/software/bioinf/hmmgene

16-Sep-2008

LION-XB

1.1

http://rcc.its.psu.edu/hpc/software/bioinf/hmmgene

16-Sep-2008

LION-XC

1.1

http://rcc.its.psu.edu/hpc/software/bioinf/hmmgene

16-Sep-2008

LION-XD

1.1

http://rcc.its.psu.edu/hpc/software/bioinf/hmmgene

16-Sep-2008

LION-XJ

1.1

http://rcc.its.psu.edu/hpc/software/bioinf/hmmgene

16-Sep-2008

LION-XO

1.1

http://rcc.its.psu.edu/hpc/software/bioinf/hmmgene

16-Sep-2008

Versions listed in bold are the default version.


MrBayes

John P. Huelsenbeck and Fredrik Ronquist

MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.

MrBayes is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

3.1.2

http://rcc.its.psu.edu/hpc/software/bioinf/mrbayes

16-Sep-2008

LION-XB

3.1.2

http://rcc.its.psu.edu/hpc/software/bioinf/mrbayes

16-Sep-2008

LION-XC

3.1.2

http://rcc.its.psu.edu/hpc/software/bioinf/mrbayes

16-Sep-2008

LION-XD

3.1.2

http://rcc.its.psu.edu/hpc/software/bioinf/mrbayes

16-Sep-2008

LION-XJ

3.1.2

http://rcc.its.psu.edu/hpc/software/bioinf/mrbayes

16-Sep-2008

LION-XO

3.1.2

http://rcc.its.psu.edu/hpc/software/bioinf/mrbayes

16-Sep-2008

Versions listed in bold are the default version.


MZEF

Cold Spring Harbor Laboratory

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.

MZEF is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

http://rcc.its.psu.edu/hpc/software/bioinf/mzef

16-Sep-2008

LION-XB

http://rcc.its.psu.edu/hpc/software/bioinf/mzef

16-Sep-2008

LION-XC

http://rcc.its.psu.edu/hpc/software/bioinf/mzef

16-Sep-2008

LION-XD

http://rcc.its.psu.edu/hpc/software/bioinf/mzef

16-Sep-2008

LION-XJ

http://rcc.its.psu.edu/hpc/software/bioinf/mzef

16-Sep-2008

LION-XO

http://rcc.its.psu.edu/hpc/software/bioinf/mzef

16-Sep-2008

Versions listed in bold are the default version.


PHYLIP

University of Washington Dept. of Genome Sciences

PHYLIP is a package of programs for inferring phylogenies.

PHYLIP is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

3.67

http://rcc.its.psu.edu/hpc/software/bioinf/phylip

16-Sep-2008

LION-XB

3.67

http://rcc.its.psu.edu/hpc/software/bioinf/phylip

16-Sep-2008

LION-XC

3.67

http://rcc.its.psu.edu/hpc/software/bioinf/phylip

16-Sep-2008

LION-XD

3.67

http://rcc.its.psu.edu/hpc/software/bioinf/phylip

16-Sep-2008

LION-XJ

3.67

http://rcc.its.psu.edu/hpc/software/bioinf/phylip

16-Sep-2008

LION-XO

3.67

http://rcc.its.psu.edu/hpc/software/bioinf/phylip

16-Sep-2008

Versions listed in bold are the default version.


ReadSeq

Indiana University Dept. of Biology

Converts input DNA/AA sequence to specified format.

ReadSeq is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

2.1.24

http://rcc.its.psu.edu/hpc/software/bioinf/readseq

16-Sep-2008

LION-XB

2.1.24

http://rcc.its.psu.edu/hpc/software/bioinf/readseq

16-Sep-2008

LION-XC

2.1.24

http://rcc.its.psu.edu/hpc/software/bioinf/readseq

16-Sep-2008

LION-XD

2.1.24

http://rcc.its.psu.edu/hpc/software/bioinf/readseq

16-Sep-2008

LION-XJ

2.1.24

http://rcc.its.psu.edu/hpc/software/bioinf/readseq

16-Sep-2008

LION-XO

2.1.24

http://rcc.its.psu.edu/hpc/software/bioinf/readseq

16-Sep-2008

Versions listed in bold are the default version.


SEG

National Center for Biotechnology Information

SEG divides sequences into contrasting segments of low-complexity and high-complexity.

SEG is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

http://rcc.its.psu.edu/hpc/software/bioinf/seg

16-Sep-2008

LION-XB

http://rcc.its.psu.edu/hpc/software/bioinf/seg

16-Sep-2008

LION-XC

http://rcc.its.psu.edu/hpc/software/bioinf/seg

16-Sep-2008

LION-XD

http://rcc.its.psu.edu/hpc/software/bioinf/seg

16-Sep-2008

LION-XJ

http://rcc.its.psu.edu/hpc/software/bioinf/seg

16-Sep-2008

LION-XO

http://rcc.its.psu.edu/hpc/software/bioinf/seg

16-Sep-2008

Versions listed in bold are the default version.


sim4

Comp. Sci. and Engr. and Biochem. and Mol. Bio. at Penn State Univ.

sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene.

sim4 is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

2001-10-12

No on-line instructions available

16-Sep-2008

LION-XB

2001-10-12

No on-line instructions available

16-Sep-2008

LION-XC

2001-10-12

No on-line instructions available

16-Sep-2008

LION-XD

2001-10-12

No on-line instructions available

16-Sep-2008

LION-XJ

2001-10-12

No on-line instructions available

16-Sep-2008

LION-XO

2001-10-12

No on-line instructions available

16-Sep-2008

Versions listed in bold are the default version.


Sputnik

University of Washington Dept. of Molecular Biotechnology

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.

Sputnik is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

http://rcc.its.psu.edu/hpc/software/bioinf/sputnik

16-Sep-2008

LION-XB

http://rcc.its.psu.edu/hpc/software/bioinf/sputnik

16-Sep-2008

LION-XC

http://rcc.its.psu.edu/hpc/software/bioinf/sputnik

16-Sep-2008

LION-XD

http://rcc.its.psu.edu/hpc/software/bioinf/sputnik

16-Sep-2008

LION-XJ

http://rcc.its.psu.edu/hpc/software/bioinf/sputnik

16-Sep-2008

LION-XO

http://rcc.its.psu.edu/hpc/software/bioinf/sputnik

16-Sep-2008

Versions listed in bold are the default version.


Treetool

Ribosomal Database Project

Treetool is an interactive tool for displaying, editing, and printing phylogenetic trees.

Treetool is available on the following HPC machines:

Machine Version Instructions Last Update

Hammer

2.0.2

http://rcc.its.psu.edu/hpc/software/bioinf/treetool

16-Sep-2008

LION-XB

2.0.2

http://rcc.its.psu.edu/hpc/software/bioinf/treetool

16-Sep-2008

LION-XC

2.0.2

http://rcc.its.psu.edu/hpc/software/bioinf/treetool

16-Sep-2008

LION-XD

2.0.2

http://rcc.its.psu.edu/hpc/software/bioinf/treetool

16-Sep-2008

LION-XJ

2.0.2

http://rcc.its.psu.edu/hpc/software/bioinf/treetool

16-Sep-2008

LION-XO

2.0.2

http://rcc.its.psu.edu/hpc/software/bioinf/treetool

16-Sep-2008

Versions listed in bold are the default version.



Please send questions or suggestions about this web page to beatnic@aset.psu.edu

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