| AlignACE |
1.0 |
Motif related |
Aligns Nucleic Acid Conserved Elements - finds sequence elements conserved in a set of DNA sequences using a Gibbs sampling strategy. Accessory programs are also installed |
Local
External |
| arrayOligoSelector |
3.8.4 |
Oligo design |
Design gene specific long oligonucleotide probes |
Local
External |
| Augustus |
1.8.2 |
Gene Finding |
Predict genes in eukaryotic genomic sequences. |
Local
External |
| AVID |
2.1 |
Alignment |
Global alignment method for sequence alignments of large genomic regions up to megabases long. AVID is a pairwise alignment program and MAVID is a multiple alignment program. |
Local
External |
| Blast |
2.2.13 |
Alignment |
Basic Local Alignment Search Tool for sequence database searching. The blastall tool and associated utilities like formatdb and bl2seq are available from the command line. Initializing the tool will also initialize the local formatted databases for usage with blast located at /bioportal/db/blast (eg. -d nr or -d dmel/dmel-all-transcript-r4.3.fasta) |
Local
External |
| Blat |
3.2 |
Alignment |
BLAST-Like Alignment Tool it offers a faster, less sensitive alternative to BLAST |
Local
External |
| CAP3 |
1.0 |
EST manipulation |
DNA Sequence Assembly Program. It has 2 executables cap3 and formcon.
New Ace File Format is available at aceform |
Local
External |
| CLOBB |
2.0 |
Alignment |
A program for clustering sequences on the basis of BLAST similarity. This program takes a set of DNA sequences and clusters them into groups which putatively derive from the same gene. |
Local
External |
| Clover |
2006.03.27 |
Motif related |
Cis-eLement OVERrepresentation is a program for identifying functional sites in DNA sequences |
External |
| Clustalw |
1.83 |
Alignment |
Multiple sequence alignment. It is computationally intensive and users should run large datasets on parallel versions of like the one on UITS supported AVIDD http://rac.uits.iu.edu/bioinformatics/. We also provide a web-interface for clustalw generated using PISE which should be used for small datasets only. ClustalX uses x-windows which provides a friendly interface even on UNIX login |
Local
External |
| Consed |
15.0 |
Fragment Assembly |
X-windows viewer and editor for assembled shotgun sequence data from phrap |
Local
External |
| Emboss |
3.0 |
Miscellaneous |
Emboss suite of tools. EMBOSS Explorer is the web-interface we provide to access the emboss suite of tools |
Local
External |
| EMnEM |
1.0 |
Motif related |
Expectation-Maximization on Evolutionary Mixtures for phylogenetic motif detection. Need to copy evm.ctl to working directory from /bioportal/sw/share/emnem/dat/ |
Local
External |
| ESTScan |
2.0 |
EST manipulation |
Detect and reconstruct coding regions from EST sequences |
Local
External |
| FASTA |
3.4 |
Alignment |
Sequence database search tool which is slower than BLAST but more accurate. We also provide some utilities like align0 which came with previous versions of FASTA. Some FASTA sequences which can be useful in general are provided at /bioportal/db/fasta |
Local
External |
| FastDNAml |
1.2.2 |
Phylogeny |
Program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. It is computationally intensive and users should run large datasets on parallel versions like the one on UITS supported AVIDD http://rac.uits.iu.edu/bioinformatics/ |
Local
External |
| GCG |
11.0 |
Miscellaneous |
Large suite of tools that perform various protein and nucleic acid sequence analysis. We provide W2H web-interface and Seqlab X-windows interface to GCG and also maintain the latest databases like Genbank, PIR, UniProt, Pfam and REBASE |
Local
External |
| GeneTraffic |
3.2.11 |
Miscellaneous |
Import, examine and run statistical analysis on standard two-color ratio-based microarray. |
Local
External |
| GHMM |
0.7.0 |
Miscellaneous |
General Hidden Markov Model library implements data structures and algorithms for basic and extended HMMs |
Local
External |
| Glimmer |
3.02 |
Gene Finding |
Finding genes in microbial DNA. It takes a sequence and a set of Markov models for genes and outputs a list of ORFs. We also provided its web-interfaces made using PISE |
Local
External |
| HMM |
2.3.2 |
Miscellaneous |
Profile Hidden Markov Models for biological sequence analysis |
Local
External |
| InParanoid |
1.35 |
Miscellaneous |
Tool to identify orthologs while differentiating between inparalogs and outparalogs. |
Local
External |
| Lagan |
1.21 |
Alignment |
Highly parametrizable pairwise global alignment program. It takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors. |
Local
External |
| lucy |
1.19p |
Fragment Assembly |
A Sequence Cleanup Program, it is a utility that prepares raw DNA sequence fragments for sequence assembly |
Local
External |
| Mapmaker |
3.0 |
Miscellaneous |
Constructing Genetic Linkage Maps |
Local
External |
| MatCompare |
1.1 |
Motif related |
Provides methods for comparing transcription factor binding site (TFBS) position frequency matrices (PFMs). The user has a choice of using the Kullback-Leibler divergence, the chi squared test or the Fisher-Irwin exact test of similarity. |
Local
External |
| MatrixReduce |
1.0 |
Motif related |
Use genome-wide occupancy data for a transcription factor (e.g. ChIP-chip or mRNA expression data) and associated nucleotide sequences to discover the sequence-specific binding affinity of the transcription factor. |
Local
External |
| MDscan |
1.0 |
Motif related |
Motif Discovery scan examines the ChIP-array selected sequences and searches for DNA sequence motifs representing the protein-DNA interaction sites. |
Local
External |
| MEME |
3.5.4 |
Motif related |
Discover motifs (highly conserved regions) in groups of related DNA or protein sequences
Commands to run on csh/tcsh
>source /bioportal/sw/encap/meme-3.5.4/etc/meme.csh
>/bioportal/sw/encap/meme-3.5.4/bin/meme.bin |
External |
| Monkey |
2.0 |
Motif related |
Program designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors |
Local
External |
| Motifregressor |
1.0 |
Sequence Manipulation |
Program for finding DNA sequence motifs using Expression data |
Local
External |
| MrBayes |
3.1.2 |
Phylogeny |
Program for the Bayesian estimation of phylogeny that takes as input a character matrix in a NEXUS file format |
Local
External |
| NNPP |
2.2 |
Motif related |
Neural Network Promoter Prediction |
Local
External |
| oligoArray |
2.1 |
Oligo design |
Computes gene specific oligonucleotides for genome scale oligonucleotide microarray construction |
Local
External |
| OligoPicker |
2.3.2 |
Oligo design |
A tool for selecting up to five oligo probes for each DNA sequence |
Local
External |
| PAML |
3.15 |
Phylogeny |
Copy (cp -L) the /bioportal/sw/share/paml/dat folder and the necessary files (like .ctl) from /bioportal/sw/bin to the working directory |
Local
External |
| Partigene |
3.0.1 |
EST manipulation |
Software for processing sequences (usually ESTs) into clusters representing putative genes, and for annotating and databasing them |
Local
External |
| Patser |
3e |
Motif related |
Find locations of patterns in sequence. This program scores the L-mers (subsequences of length L) of the
indicated sequences against the indicated alignment or weight matrix |
Local
External |
| Paup |
4.0 |
Phylogeny |
Phylogenetic Analysis Using Parsimony. It is a software package for the inference of evolutionary trees |
Local
External |
| phd2fasta |
0.990622.f |
Fragment Assembly |
Reads phred files and writes sequence and quality value FASTA files. It acts as a pipe between phred and phrap |
Local
External |
| phrap |
0.960731 |
Fragment Assembly |
Program for assembling shotgun DNA sequence data. It comes with crossmatch and swat sequence comparison files |
Local
External |
| phred |
0.020425.c |
Fragment Assembly |
Reads DNA sequencer trace data, calls bases, assigns quality values to the bases |
Local
External |
| Phylip |
3.6 |
Phylogeny |
PHYLogeny Inference Package used for phylogenetic analysis. It is computationally intensive and users should run large datasets on parallel versions like the one on UITS supported AVIDD http://rac.uits.iu.edu/bioinformatics/ |
Local
External
|
| PhyloGibbs |
1.2 |
Motif related |
Find binding sites for transcription factors in cis-regulatory sequences of DNA based on gibbs sampling algorithm |
Local
External |
| PhyloNet |
2b |
Motif related |
Phylogenetic Regulatory Network - a motif discovery program based on sequences of several evolutionarily related genomes |
Local
External |
| Phyml |
2.4.4 |
Phylogeny |
Estimate large phylogenies by maximum likelihood |
Local
External |
| PoSSuM |
1.2a |
Motif related |
Position specific scoring matrices matching using fast index based algorithms |
Manual
External |
| Predator |
2.1 |
Miscellaneous |
Protein secondary structure prediction from single sequence or a set of sequences |
Local
External |
| primer3 |
1.0.0 |
Miscellaneous |
Pick primers for PCR reactions |
Local
External |
| ProDA |
1.0 |
Miscellaneous |
Protein Domain Aligner is a software for generating multiple alignments of protein sequences with repeats and rearrangements, e.g. proteins with multiple domains. |
External |
| Prot4EST |
2.2 |
EST manipulation |
Translating Expressed Sequence Tags from neglected genomes. Pipeline tool needed for ESTScan. (Type prot4EST_2.2.pl at the command prompt) |
Local
External |
| readseq2 |
2 |
Sequence Manipulation |
Sequence format converter |
Local
External |
| Repeatmasker |
3.1.5 |
Sequence Manipulation |
Screens DNA sequences for interspersed
repeats and low complexity DNA sequences. The repbase library is available at /bioportal/sw/share/repeatmasker/Libraries |
Local
External |
| RMES |
2.1.6 |
Motif related |
Programs to detect words that appear in a DNA sequence with an unexpected frequency |
External
|
| RRTree |
1.1 |
Phylogeny |
RRTree is a program for relative-rate tests. It compares substitution rates between DNA or protein sequences grouped in phylogenetically defined lineages |
Local
External |
| Scan_for_matches |
1.0 |
Sequence Manipulation |
PatScan pattern matcher used for searching protein or nucleotide sequence archives |
Local
External |
| SeqClean |
1.0 |
EST manipulation |
Tool for validation and trimming of DNA sequences from a flat
file database (FASTA format). SeqClean was designed primarily for "cleaning"
of EST databases |
Local
External |
| seqio |
1.2.2 |
Sequence Manipulation |
Read/write biological sequence files in various file formats |
Local
External |
| sim4 |
2003.09.21 |
EST manipulation |
Aligns an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene |
Local
External |
| Spidey |
1.0 |
Alignment |
An mRNA-to-genomic alignment program |
External |
| Tcoffee |
1.37 |
Alignment |
Multiple sequence alignment. The executables that can be used are extract_from_pdb, mocca, test.pl, lalign2list and t_coffee |
Local
External |
| TRANSFAC |
9.2 |
Miscellaneous |
Database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Provided through the web-interface along with Match and Patch tools |
Local
External |
| Tree_Puzzle |
5.2 |
Phylogeny |
Program to construct phylogenetic trees from molecular sequence data by maximum likelihood. It is computationally intensive and users should run large datasets on parallel versions like the one on UITS supported AVIDD http://rac.uits.iu.edu/bioinformatics/ |
Local
External |
| TREG Comparator |
1.0 |
Motif related |
Allows one to compare a set of position weight matrices (PWM) against the T-Reg database |
Local
External |
| tRNAscan |
1.23 |
Gene Finding |
Search for tRNA genes in genomic sequence |
Local
External |
| unafold |
3.3 |
Oligo design |
The UNAFold package contains several programs for performing energy minimizationand partition function calculations on nucleic acid sequences. Among the programs is a Perl script, hybrid2.pl, which simulates a one- or two-sequence ensemble of species by running other programs as appropriate. |
Local
External |
| VCE |
5.1.2 |
Miscellaneous |
Estimate covariance matrices |
Local
External |
| ViennaRNA |
1.6.1 |
Miscellaneous |
Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures |
Local
External |
| Vista |
1.4.26 |
Alignment |
Tool for visualizing global DNA sequence alignments of arbitrary length |
Local
External |
| Vmatch |
2004.03.10 |
Sequence Manipulation |
Large scale sequence analysis software |
Local
External |
| Weblogo |
2.8.2 |
Miscellaneous |
Make sequence logo plot. Initialized by executing 'use seqlogo' |
Local
External |
| WU-Blast |
2.0 |
Alignment |
Sequence database search tool supported by Washington University. Initialized by executing 'use blast' |
Local
External |
