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HMMER

Profile hidden Markov models for biological sequence analysis. Find HMMER at: http://hmmer.janelia.org/

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Rating: 4.7. From 10 votes.
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Dynamite

Dynamite is a code generating language developed for sequence comparison methods. Find Dynamite at: http://www.sanger.ac.uk/Software/Dynamite/

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Rating: 4.7. From 3 votes.
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Wise2

Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns. Find Wise2 at: http://www.sanger.ac.uk/Software/Wise2/

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Rating: 4.3. From 4 votes.
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JAligner – Java implementation of biological sequence alignment algorithms

JAligner is a Java implementation of biological sequence alignment algorithms. Presently, the package implements the pair wise alignment algorithm Smith-Waterman. The basic Dynamic Programming Smith-Waterman algorithm has been modified to support affine (open and extend) gap penalty. Also, Gotoh’s improvement … Continue reading

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Rating: 4.2. From 16 votes.
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E-CELL

E-CELL Simulation Environment (E-CELL SE) is a software package for cellular and biochemical modeling and simulation. Find E-CELL at: http://www.bioinformatics.org/e-cell/

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Rating: 4.2. From 13 votes.
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GENtle

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. Find GENtle at: http://gentle.magnusmanske.de

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Rating: 4.1. From 24 votes.
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VLinux

VLinux is a Linux Live CD for Bioinformatics. It contains various sequence and structure analysis tools. The following packages are included in the present VLinux distribution. EMBOSS,GDE,Rasmol,PyMOL,GROMACS,Phylip,Arka/Genpak,ClustalW/ClustalX,TCoffee, Seaview,Garlic, Ramachandran Plot viewer, Primer, XMolCalc, NJPlot etc Find VLinux at: http://bioinformatics.org/vlinux

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Rating: 4.0. From 13 votes.
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Jalview

Jalview is a multiple alignment editor written entirely in java. Find Jalview at: http://www.ebi.ac.uk/~michele/jalview/

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Rating: 4.0. From 7 votes.
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PhyloSort

A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units. Find PhyloSort at: http://phylosort.sourceforge.net

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Rating: 4.0. From 3 votes.
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DEODAS

DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides Find DEODAS at: http://deodas.sourceforge.net/

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Rating: 4.0. From 2 votes.
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