These programs are available for free download and occasional use, as defined below, by academic users. Corporate users can download the software for evaluation purposes only.
The downloaded software is copyright Softberry, Inc. and is protected by intellectual property laws and treaties.
User is permitted to download, install and run the software for use in academic research projects as a single user. Free use is limited to 50 runs per program per user per year, for heavier use, please contact Softberry for a license (Email: softberry@softberry.com). No commercial use of the software is permitted without a license. User is not permitted to sell or distribute the software or its elements, including logos, trademarks and data, in any form, modify, decompile or reverse-engineer the software, or create any derivative works based on it.
The user should reference the used software when publishing or present the project results (as a reference given in doc file or Web link to the download page,
This software is provided on "as is, with all defects" basis. Any express or implied warranties, including, but not limited to, fitness for a particular purpose are disclaimed. In no event shall Softberry be liable for any direct or indirect damages, including, but not limited to, loss of use, data, profits, or business interruption.
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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ReadsMap
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View
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Download
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Download
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Download
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Reads Mapping Viewer
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Mapping of reads to chromosome (contig)
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Reads Mapping Viewer
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View
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Download
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Download
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Download
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The "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data.
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Assembler
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View
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Download
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Download
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Download
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Assember Viewer
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Algorithm of ab initio genome assembling using data produced by next-generation sequencing machines (Illumina/Solexa/etc). To view the program output data the Assembler Viewer can be used.
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Assembler Viewer
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View
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Download
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Download
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Download
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The "Assembler Viewer" software is developed to visualize the "Assembler" output data.
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SNP-Toolbox
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View
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Download
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Download (4.3Gb)
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Download (W) (3.8GB)
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A fast and effective tool for analysis of genome variations in human chromosomes.
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Visan
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View
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Download
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Download (Win)
Download (Mac)
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Visan - data classification and visualization package.
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Promoter
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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CPGFinder
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View
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Download
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Download
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Download
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Search for CpG islands in sequences
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FPROM
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View
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Download
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Download
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Download
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Human promoter prediction
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Nsite
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View
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Download
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Download
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Download
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Search for of consensus patterns with statistical estimation.
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Nsite-h
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View
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Download
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Download
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Download
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Search for statistically nonrandom and conservative motifs of human/animal and plant transcription Regulatory Elements (REs) available in both of aligned orthologous/homologous DNA sequences.
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Nsite-m
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View
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Download
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Download
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Download
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Search for regulatory motifs conserved in several sequences
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Pattern
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View
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Download
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Download
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Download
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Search for significant patterns in the set of sequences.
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Polyah
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View
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Download
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Download
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Download
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Recognition of 3'-end cleavage and polyadenilation region
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ScanWM-PL
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View
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Download
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Download
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Download
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Search for weight matrix patterns of plant regulatory sequences
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TSSG
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View
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Download
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Download
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Download
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Recognition of human PolII promoter region and start of transcription
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Protein Structure
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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3D-Comp
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View
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Download
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Download
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Download
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3D-Explorer
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Sequence Alignment to Superposition
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3D-Match
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View
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Download
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Download
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Download
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3D-Explorer
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Pairwise protein structure alignment
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3D-ModelFit
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View
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Download
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Download
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Download
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3D-Explorer
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Program for the estimation of quality of 3D model structure of protein.
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Abini3D
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View
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Download
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Download
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Download
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3D-Explorer
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Ab inition folding
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CysRec
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View
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Download
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Download
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Download
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Prediction of SS-bonding states of cysteines and disulphide bridges in protein sequences
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GetAtoms
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View
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Download
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Download
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Download
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3D-Explorer
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Optimization of replaced side chain groups by simulated annealing algorithm
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MolDyn
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View
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Download
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Download
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Download
Download (W)
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3D-Explorer
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MolDyn is designed to perform multiple tasks with protein structure.
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MolMech
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View
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Download
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Download
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Download
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3D-Explorer
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Energy minimization program by molecular mechanic
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NNSSP
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View
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Download
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Download
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Download
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Nearest-neighbor SS prediction
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Net-SSPredict
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View
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Download
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Download
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Download
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Program for secondary structure prediction. Neural nets based on profile of psiBLAST comparison of the query sequence with NR database.
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PDisorder
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View
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Download
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Download
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Download
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Program for predicting ordered and disordered regions in protein sequences
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SSEnvID
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View
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Download
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Download
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Download
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Protein secondary structure and environment assignment from atomic coordinates
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SSP
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View
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Download
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Download
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Download
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Prediction of a-helix and b-strand segments of globular proteins
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SSPAL
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View
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Download
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Download
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Download
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Prediction of protein secondary sturcture by using local alignments
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Alignments
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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Protmap
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View
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Download
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Download
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Download
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Mapping of a set of proteins on genome
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MaliN
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View
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Download
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Download
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Download
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MaliN Viewer
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Multiple alignment for nucleotide sequences.
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MaliP
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View
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Download
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Download
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Download
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MaliP Viewer
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Multiple alignment for protein sequences.
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EstMap
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View
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Download
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Download
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Download
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Program for mapping a whole set of mRNAs/ESTs to a chromosome sequence
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Scan2
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View
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Download
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Download
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Download
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Program for aligning two multimegabyte-size genome sequences using a sequential search for most significant similarity regions.
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Scan2a
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View
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Download
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Download
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Download
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Program for aligning two aminoacid sequences using a sequential search for most significant similarity regions.
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Gene Finding
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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Fex
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View
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Download
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Download
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Download
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Prediction of internal, 5'- and 3'- exons in Human DNA sequences.
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Fgenes
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View
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Download
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Download
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Download
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Sequence Explorer, PDFGenes
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Pattern based human gene structure prediction (multiple genes, both chains).
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Fgenes-m
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View
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Download
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Download
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Download
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Sequence Explorer, PDFGenes
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Pattern-based prediction of multiple variants of gene structure
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Fsplice
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View
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Download
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Download
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Download
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Program provides the possibility to search for both donor and acceptor sites, and to define thresholds for them independently. Program allows to search minor variants of splicing donor site (GC-site) as well.
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PDFGenes
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View
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Download
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Download
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Download
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PDFGenes utilizes the results of Gene Finding software, such as FGenesh, FGenesh+, FGenesh-C, FGenesh-2, FGenes, FGenes-m and BestORF, and represents them in PDF format for better viewability.
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PSF
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View
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Download
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Download
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Download
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Finding pseudogenes in a genomic sequence.
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Rnaspl
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View
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Download
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Download
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Download
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Program for predicting exon-exon junction positions in cDNA sequences. For this program gcc fortran library should be installed locally.
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SPL
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View
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Download
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Download
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Download
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Prediction of splice sites in DNA sequences. For this program gcc fortran library should be installed locally.
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SplM
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View
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Download
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Download
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Download
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Prediction of splice sites in Human DNA sequences.
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Bacterial Gene Finding
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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ABSplit
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View
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Download
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Download
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Download
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Sequence Explorer
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Program determines for the nucleotide sequence of approx. 300-600 n.p. whether it belongs to archeal or bacterial genome.
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Bprom
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View
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Download
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Download
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Download
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Prediction of bacterial promoters
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FindTerm
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View
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Download
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Download
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Download
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RNA Secondary Structure Viewer
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Searchs for bacterial terminators in DNA sequences.
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RNA Strucuture
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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Bestpal-E
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View
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Download
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Download
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Download
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Calculates best palindrome for given RNA sequence, and also a set suboptimal palindromes (sorted by energy)
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Bestpal-H
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View
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Download
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Download
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Download
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RNA Secondary Structure Viewer
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Calculates best palindrome for given RNA sequence with restrictions.
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Bestpal-W
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View
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Download
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Download
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Download
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RNA Secondary Structure Viewer
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Program for searching best "linear" RNA secondary structure for long sequences with a window moving along the sequence.
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Find-miRNA
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View
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Download
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Download
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Download
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Searchs for pre-miRNAs in a given RNA sequence and for miRNA in each found pre-miRNA.
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FoldRNA
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View
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Download
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Download
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Download
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RNA Secondary Structure Viewer
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Program for RNA secondary structure prediction based on dynamic programming (Nussinov and Jackonson, 1978, Zuker, 2005). |
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Protein Location
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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PSite
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View
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Download
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Download
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Download
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Search for of prosite patterns with statistical estimation.
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CTL-Epitope
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View
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Download
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Download
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Download
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This program is designed for prediction of CTL epitopes of length=9 in protein sequences.
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Protcomp-AN
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View
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Download
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Download
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Download
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Program for Identification of sub-cellular localization of Eukaryotic proteins: Animal/Fungi.
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Protcomp-B
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View
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Download
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Download
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Download
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Program for Identification of sub-cellular localization of bacterial proteins.
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Protcomp-PL
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View
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Download
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Download
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Download
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Program for Identification of sub-cellular localization of Eukaryotic proteins: Plants
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Repeats
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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LCRep
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View
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Download
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Download
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Download
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Sequence Explorer
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Program for mapping low complexity regions in nucleotide sequences.
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LCRep-P
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View
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Download
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Download
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Download
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Sequence Explorer
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Program for mapping low complexity regions in protein sequences.
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TandemRep
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View
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Download
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Download
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Download
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Program for mapping the Tandem Repeats Regions in nucleotide sequences.
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TandemRep-P
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View
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Download
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Download
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Download
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Program for mapping the Tandem Repeats Regions in protein sequences.
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SelTag
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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BdClust
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View
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Download
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Download
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Download
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Clustering of gene expression profiles or samples by Ben-Dor algorithm.
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CHPImport
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View
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Download
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Download
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Download
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Import expression data from the Affymetrix CHP format to SelTag data file.
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FieldCorr
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View
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Download
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Download
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Download
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Graph Viewer
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The program calculates correlation coefficients between the gene expression values in experiments (fields).
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GeneCorr
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View
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Download
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Download
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Download
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Graph Viewer
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The program calculates correlation coefficients between the gene expression profiles.
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HClust
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View
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Download
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Download
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Download
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Clustering of gene expression profiles by hierarchical algorithm.
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Mas5Norm
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View
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Download
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Download
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Download
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Normalization of the Affymetrix gene expression row data by MAS 5.0 algorithm.
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Mas5Baseline
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View
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Download
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Download
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Download
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Comparison of the Affymetrix gene expression row data to the baseline data by MAS 5.0 algorithm.
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SelByExpr
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View
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Download
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Download
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Download
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Gene selection by query (logical expression).
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SelCorr
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View
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Download
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Download
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Download
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Graph Viewer
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The program selects most correlated genes for specified gene set.
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SOMClust
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View
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Download
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Download
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Download
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The program clusters gene expression profiles or samples by SOM (Self-Organizing Map) algorithm.
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Statistics
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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SNNBP-Learn
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View
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Download
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Download
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Download
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SNNBP-Learn implement the back-propagation training algorithm and output the optimal NN structure, saved in the SNNBP internal format.
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SNNBP-Predict
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View
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Download
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Download
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Download
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SNNBP-Predict - neural network calculate output values (predictions) using input values from the data file (target values need not be specified in this option).
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SNNBP-Test
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View
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Download
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Download
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Download
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SNNBP-Test implement testing of the previously obtained network on the user data.
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Seqman
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Restrictase
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View
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Download
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Download
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Download
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Restrictase Viewer
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The program for finding and displaying the positions of the cut sites of restriction enzyme recognition sequences.
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Viewers
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Program name
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Help
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Documentation
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Linux
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Mac/Windows (W)
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Results Viewer
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Title
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3D-Explorer
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View
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Download
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Download
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Download
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3D Explorer is designed to visualize spatial models of biological macromolecules and their complexes. Application is compatible with PDB files.
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Assembler Viewer
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View
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Download
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Download
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Download
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The "Assembler Viewer" software is developed to visualize the "Assembler" output data.
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GenomeMatch Viewer
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View
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Download
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Download
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Download (Mac)
Download (Win)
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GenomeMatch Viewer provides the possibility to visualize the sites of homology between the sets of sequences.
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Graph Viewer
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View
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Download
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Download
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Download
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The application is made for visualization of statistics files.
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MaliN Viewer
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View
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Download
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Download
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Download
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The "MaliN viewer" application is developed for aligning nucleotide sequences and working with results of such alignments.
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MaliP Viewer
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View
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Download
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Download
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Download
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The "MaliP viewer" application is developed for aligning protein sequences and working with results of such alignments.
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Reads Mapping Viewer
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View
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Download
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Download
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Download
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The "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data.
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Restrictase Viewer
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View
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Download
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Download
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Download
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The "Restrictase viewer" application is purposed for visualization of restriction sites that were found with use of "Restrictase" program.
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RNA Secondary Structure Viewer
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View
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Download
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Download
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Download
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RNA Secondary Structure Viewer is made for visualization and manipulation of RNA secondary structure.
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Sequence Explorer
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View
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Download
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Download
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Download
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Sequence Explorer provides the visual representation of genome annotations.
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