Free download Softberry programs for Academia researchers.

Softberry Programs available to academic users at no charge for occasional use in research projects.

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.

By downloading the software, users agree to the following terms of use:

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.

Some programs require local installation of GCC Fortran library.

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.

Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
Adapter_Trim View Download Download The adapter_trim main goal is removing adapters from reads, but you can use it for the task of searching and removing polyN tails and cutting sequence by quality.
GenomeMatch View Download Download Build synteny alignments of 2 genomes.
pairDistance View Download Download pairDistance - Programs for collect, analyze and visualization pair-ends reads distance
ReadsClean View Download Download ReadsClean: The Package for Purging Random Errors from Large Volumes of Short Sequences (reads)
ReadsMap View Download Download Reads Mapping Viewer Mapping of reads to chromosome (contig)
Reads Mapping Viewer View Download Download Download   The "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data.
Transcripts Assembler (TRA) View Download Download Assember Viewer Transcripts Assembler (TRA) - Assembly of transcripts from RNASeq reads (without genome sequence information)
Assembler Viewer View Download Download Download   The "Assembler Viewer" software is developed to visualize the "Assembler" output data.
SNP-Toolbox View Download Download (4.3Gb) Download  (W) (3.8GB)   A fast and effective tool for analysis of genome variations in human chromosomes.
Visan View Download Download  (Win)

Download  (Mac)
  Visan - data classification and visualization package.
Promoter
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
CPGFinder View Download Download Download   Search for CpG islands in sequences
FPROM View Download Download Download   Human promoter prediction
Nsite View Download Download Download   Search for of consensus patterns with statistical estimation.
Nsite-h View Download Download Download   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.
Nsite-m View Download Download Download   Search for regulatory motifs conserved in several sequences
Pattern View Download Download Download   Search for significant patterns in the set of sequences.
Polyah View Download Download Download   Recognition of 3'-end cleavage and polyadenilation region
ScanWM-PL View Download Download Download   Search for weight matrix patterns of plant regulatory sequences
TSSG View Download Download Download   Recognition of human PolII promoter region and start of transcription
TSSPlant View Download Download   Search for RNA polymerase II promoters (TSSs) in plant DNA sequences
Protein Structure
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
3D-Comp View Download Download Download 3D-Explorer Sequence Alignment to Superposition
3D-Match View Download Download Download 3D-Explorer Pairwise protein structure alignment
3D-ModelFit View Download Download Download 3D-Explorer Program for the estimation of quality of 3D model structure of protein.
Abini3D View Download Download Download 3D-Explorer Ab inition folding
CysRec View Download Download Download   Prediction of SS-bonding states of cysteines and disulphide bridges in protein sequences
GetAtoms View Download Download Download 3D-Explorer Optimization of replaced side chain groups by simulated annealing algorithm
MolDyn View Download Download Download
Download (W)
3D-Explorer MolDyn is designed to perform multiple tasks with protein structure.
MolMech View Download Download Download 3D-Explorer Energy minimization program by molecular mechanic
NNSSP View Download Download Download   Nearest-neighbor SS prediction
Net-SSPredict View Download Download Download   Program for secondary structure prediction. Neural nets based on profile of psiBLAST comparison of the query sequence with NR database.
PDisorder View Download Download Download   Program for predicting ordered and disordered regions in protein sequences
SSEnvID View Download Download Download   Protein secondary structure and environment assignment from atomic coordinates
SSP View Download Download Download   Prediction of a-helix and b-strand segments of globular proteins
SSPAL View Download Download Download   Prediction of protein secondary sturcture by using local alignments
Alignments
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
Protmap View Download Download Download   Mapping of a set of proteins on genome
MaliN View Download Download Download MaliN Viewer Multiple alignment for nucleotide sequences.
MaliP View Download Download Download MaliP Viewer Multiple alignment for protein sequences.
EstMap View Download Download Download   Program for mapping a whole set of mRNAs/ESTs to a chromosome sequence
Scan2 View Download Download Download   Program for aligning two multimegabyte-size genome sequences using a sequential search for most significant similarity regions.
Scan2a View Download Download Download   Program for aligning two aminoacid sequences using a sequential search for most significant similarity regions.
Gene Finding
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
Fex View Download Download Download   Prediction of internal, 5'- and 3'- exons in Human DNA sequences.
Fgenes View Download Download Download Sequence Explorer, PDFGenes Pattern based human gene structure prediction (multiple genes, both chains).
Fgenes-m View Download Download Download Sequence Explorer, PDFGenes Pattern-based prediction of multiple variants of gene structure
Fsplice View Download Download Download   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.
PDFGenes View Download Download Download   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.
PSF View Download Download Download   Finding pseudogenes in a genomic sequence.
Rnaspl View Download Download Download   Program for predicting exon-exon junction positions in cDNA sequences. For this program gcc fortran library should be installed locally.
SPL View Download Download Download   Prediction of splice sites in DNA sequences. For this program gcc fortran library should be installed locally.
SplM View Download Download Download   Prediction of splice sites in Human DNA sequences.
Bacterial Gene Finding
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
ABSplit View Download Download Download Sequence Explorer Program determines for the nucleotide sequence of approx. 300-600 n.p. whether it belongs to archeal or bacterial genome.
Bprom View Download Download Download   Prediction of bacterial promoters
FindTerm View Download Download Download RNA Secondary Structure Viewer Searchs for bacterial terminators in DNA sequences.
RNA Strucuture
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
Bestpal-E View Download Download Download   Calculates best palindrome for given RNA sequence, and also a set suboptimal palindromes (sorted by energy)
Bestpal-H View Download Download Download RNA Secondary Structure Viewer Calculates best palindrome for given RNA sequence with restrictions.
Bestpal-W View Download Download Download RNA Secondary Structure Viewer Program for searching best "linear" RNA secondary structure for long sequences with a window moving along the sequence.
Find-miRNA View Download Download Download   Searchs for pre-miRNAs in a given RNA sequence and for miRNA in each found pre-miRNA.
FoldRNA View Download Download Download RNA Secondary Structure Viewer Program for RNA secondary structure prediction based on dynamic programming (Nussinov and Jackonson, 1978, Zuker, 2005).
RScan View Download Download Download (W)   RScan implements a descriptor-based method of searching for RNA motifs in arbitrary sequences. The motif is given by the topology of the secondary structure, size ranges of stems and loops, and contextual constraints. A dynamic programming scheme with a thermodynamic score is used. Additional tools are RInf and b2t. RInf estimates a frequency of motif occurrence. b2t converts a dot-bracket structure into a format understandable by RScan and RInf.
Protein Location
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
PSite View Download Download Download   Search for of prosite patterns with statistical estimation.
CTL-Epitope View Download Download Download   This program is designed for prediction of CTL epitopes of length=9 in protein sequences.
Protcomp-AN View Download Download Download   Program for Identification of sub-cellular localization of Eukaryotic proteins: Animal/Fungi.
Protcomp-B View Download Download Download   Program for Identification of sub-cellular localization of bacterial proteins.
Protcomp-PL View Download Download Download   Program for Identification of sub-cellular localization of Eukaryotic proteins: Plants
Repeats
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
LCRep View Download Download Download Sequence Explorer Program for mapping low complexity regions in nucleotide sequences.
LCRep-P View Download Download Download Sequence Explorer Program for mapping low complexity regions in protein sequences.
TandemRep View Download Download Download   Program for mapping the Tandem Repeats Regions in nucleotide sequences.
TandemRep-P View Download Download Download   Program for mapping the Tandem Repeats Regions in protein sequences.
SelTag
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
BdClust View Download Download Download   Clustering of gene expression profiles or samples by Ben-Dor algorithm.
CHPImport View Download Download Download   Import expression data from the Affymetrix CHP format to SelTag data file.
FieldCorr View Download Download Download Graph Viewer The program calculates correlation coefficients between the gene expression values in experiments (fields).
GeneCorr View Download Download Download Graph Viewer The program calculates correlation coefficients between the gene expression profiles.
HClust View Download Download Download   Clustering of gene expression profiles by hierarchical algorithm.
Mas5Norm View Download Download Download   Normalization of the Affymetrix gene expression row data by MAS 5.0 algorithm.
Mas5Baseline View Download Download Download   Comparison of the Affymetrix gene expression row data to the baseline data by MAS 5.0 algorithm.
SelByExpr View Download Download Download   Gene selection by query (logical expression).
SelCorr View Download Download Download Graph Viewer The program selects most correlated genes for specified gene set.
SOMClust View Download Download Download   The program clusters gene expression profiles or samples by SOM (Self-Organizing Map) algorithm.
Statistics
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
SNNBP-Learn View Download Download Download   SNNBP-Learn implement the back-propagation training algorithm and output the optimal NN structure, saved in the SNNBP internal format.
SNNBP-Predict View Download Download Download   SNNBP-Predict - neural network calculate output values (predictions) using input values from the data file (target values need not be specified in this option).
SNNBP-Test View Download Download Download   SNNBP-Test implement testing of the previously obtained network on the user data.
Seqman
Restrictase View Download Download Download Restrictase Viewer The program for finding and displaying the positions of the cut sites of restriction enzyme recognition sequences.
Viewers
Program name Help Documentation Linux Mac/Windows (W) Results Viewer Title
3D-Explorer View Download Download Download   3D Explorer is designed to visualize spatial models of biological macromolecules and their complexes. Application is compatible with PDB files.
Assembler Viewer View Download Download Download   The "Assembler Viewer" software is developed to visualize the "Assembler" output data.
GenomeMatch Viewer View Download Download Download (Mac)

Download (Win)
  GenomeMatch Viewer provides the possibility to visualize the sites of homology between the sets of sequences.
MaliN Viewer View Download Download Download   The "MaliN viewer" application is developed for aligning nucleotide sequences and working with results of such alignments.
MaliP Viewer View Download Download Download   The "MaliP viewer" application is developed for aligning protein sequences and working with results of such alignments.
Reads Mapping Viewer View Download Download Download   The "Reads Mapping Viewer" software is developed to visualize the "ReadsMap" output data.
Restrictase Viewer View Download Download Download   The "Restrictase viewer" application is purposed for visualization of restriction sites that were found with use of "Restrictase" program.
RNA Secondary Structure Viewer View Download Download Download   RNA Secondary Structure Viewer is made for visualization and manipulation of RNA secondary structure.
Sequence Explorer View Download Download Download   Sequence Explorer provides the visual representation of genome annotations.