| Alidot |
2.05 |
The program alidot is designed to detect
conserved RNA secondary structures in small data sets of related RNA
sequences. |
| AlignIR |
|
LI-COR's AlignIR software provides sequence
alignment and assembly functions. |
| Apollo |
1.4.4 |
Apollo is a genome annotation viewer and
editor. |
| Arachne |
|
Arachne is a tool for assembling genome
sequences from whole genome shotgun reads, mostly in forward-reverse
pairs obtained by sequencing clone ends. Use of Arachne on
HPSRV.MBL.EDU is restricted to large-scale sequence assembly projects. |
| Arb |
|
The ARB software is a graphically oriented
package comprising various tools for sequence database handling and
data analysis. Arb may be installed on a number of computers, but the
important Arb databases are only maintained on GREENGENES.MBL.EDU, a
computer specifically configured for Arb. |
| Artemis |
5 |
Artemis is a free genome viewer and annotation
tool that allows visualization of sequence features and the results of
analyses within the context of the sequence, and its six-frame
translation. |
| ATV |
1.92 |
ATV (A Tree Viewer) - a phylogenetic tree
display tool. |
| BAMBUS |
2.33 |
BAMBUS is the first publicly available genome
assembly scaffolding program. |
| BLAST |
2.2.6 |
BLAST 2.0, (Basic Local Alignment Search
Tool), provides a method for rapid searching of nucleotide and protein
databases. High-throughput, parallel use of the blastall program is
provided on the Beowulf Clusters - please submit your large jobs to the
Beowulf Clusters. We maintain updated, local copies of several blast
databases. |
| CAP3 |
|
The CAP3 sequence assembler makes use of a
large number of forward-reverse constraints to locate and correct
errors in layout of sequence reads. |
| Clustalw |
1.82 |
Clustal W is a general purpose multiple
sequence alignment program for DNA or proteins. |
| Clustalx |
1.82 |
Clustal X is a new windows interface for the
ClustalW multiple sequence alignment program. |
| Cluster |
1.24 |
Cluster and TreeView are programs that provide
a computational and
graphical environment for analyzing data from DNA microarray
experiments, SAGE, or other gene expression datasets. The command line
version is invoked by hcluster. |
| COILS |
2.2 |
COILS is a program that compares a sequence to
a database of known parallel two-stranded coiled-coils and derives a
similarity score. By comparing this score to the distribution of scores
in globular and coiled-coil proteins, the program then calculates the
probability that the sequence will adopt a coiled-coil conformation. |
| Combiner |
2.12 |
The Combiner is a program that predicts gene
models using the output from other annotation software. |
| Consed |
12 |
Consed is a program for editing sequence
assemblies created with Phil Green's PHRAP assembly program, Arachne,
or other sequence assemblers supporting the ACE format. Use of Consed
on HPSRV.MBL.EDU is restricted to large-scale sequence assembly
projects. |
| CONSEL |
v0.1f |
CONSEL: for assessing the confidence of
phylogenetic tree selection |
| Critica |
1.0.5b |
CRITICA (Coding Region Identification Tool
Invoking Comparative Analysis) is a program for identifying the protein
coding regions in DNA based on a combination of evidence from dicodon
usage frequencies and a comparative analysis of the relative
conservation of DNA sequence and their potential protein products. We
highly recommend you submit large jobs to the Beowulf Clusters to take
advantage of job parallelization. |
| Cross_match |
0.990329 |
Cross-match is a general-purpose utility,
based on SWAT, for comparing any two sets of (long or short) DNA
sequences. It is most commonly used for vector screening. |
| DOTUR |
1.53 |
Distance Based OTU and Richness; DOTUR is a computer program that takes a distance matrix describing the genetic distance between DNA sequence data and assigns sequences to operational taxonomic units (OTUs) using either the furthest, average, or nearest neighbor algorithms for all possible distances that can be described using the distance matrix. Using the OTU composition data, DOTUR constructs collector's and rarefaction curves for sampling intensity, richness estimators, and diversity indices. |
| ELPH |
0.1.4 |
ELPH is a general-purpose Gibbs sampler for
finding motifs in a set of DNA or protein sequences. |
| Emboss |
2.8.0 |
EMBOSS is a free Open Source software analysis
package specially developed for the needs of the molecular biology user
community. |
| FASTA |
34 |
Many options for local alignment searches of
sequence databases. We maintain updated, local copies of several blast
databases that can be read by FASTA. |
| FastDNAml |
1.2.2 |
fastDNAml is a program for estimating maximum
likelihood phylogenetic trees from nucleotide sequences. |
| FastME |
|
FastME is a distance based phylogeny
reconstruction algorithm. |
| Fischer
perl scripts |
|
A number of small sequence manipulation
programs, including file conversion and translation. |
| Forester |
1.92 |
FORESTER is being developed as a framework for
(automated) sequence function prediction based on phylogenetic
information, e.g. phylogenomics. |
| GCcalc.pl |
|
GCCalc calculates GC content at all codon
positions, as well as 1st, 2nd, and 3rd codon positions alone. |
| GCG |
10.3 |
Molecular biologists worldwide use the GCG
Wisconsin Package as their software of choice for comprehensive
sequence analysis. This is licensed software that only runs on
GCG.MBL.EDU. The GCG databases are updated as they are provided from
the vendor. |
| GDE |
|
An integrated linux environment for
bioinformatics and evolutionary analysis based on the Genetic Data
Environment. |
| Genesplicer |
|
A fast, flexible system for detecting splice
sites in the genomic DNA of various eukaryotes. |
| GLIMMER |
2.13 |
A system for finding genes in microbial DNA,
especially the genomes of bacteria and archaea. |
| GLIMMERM |
2.5.1 |
A gene finder derived from Glimmer, but
developed specifically for eukaryotes. |
| GMEP |
1.0.1 |
Combined expression data and sequence analysis for
prediction of regulatory motifs from expression profiles.
|
| GraphViz |
1.1 |
Graphviz - open source graph drawing software |
| Hmmer |
2.3.2 |
HMMER is a freely distributable implementation
of profile HMM software for protein sequence analysis. High-throughput,
parallel use of several of the HMMER programs is provided on the
Beowulf Clusters - please submit your large jobs to the Beowulf
Clusters. We maintain updated, local copies of several Pfam databases. |
| Infernal |
0.1 |
Infernal - inference of RNA secondary
structure alignments |
| InterPro Scan |
3.3 |
InterPro is a database of protein families,
domains and functional sites in which identifiable features found in
known proteins can be applied to unknown protein sequences. |
| Jalview |
1.7.5b |
Jalview - a java multiple alignment editor |
| Jnet |
|
Jnet: A neural network protein secondary
structure prediction method. |
| JOT |
|
Random number generator
|
| Lamarc |
1.1.1 |
LAMARC is a package of programs for computing
population parameters, such as population size, population growth rate
and migration rates by using likelihoods for samples of data
(sequences, microsatellites, and electrophoretic polymorphisms) from
populations. |
| Ldhat |
|
A package for coalescent analysis of patterns
of linkage disequilibrium and estimation of the population
recombination rate |
| LUCY |
1.18p |
A sequence clean-up program (vector and
quality screening). |
| McArthur
perl scripts |
|
A variety of simple sequence and file
manipulation programs, including processing of SAGE tags. |
| Meme / Mast |
3.0.4 |
Motif discovery and search. Note, to avoid
GCG's version of MEME use memenogcg. |
| Mesquite |
|
Mesquite is software for evolutionary biology,
designed to help biologists analyze comparative data about organisms. |
| Migrate |
1.7.3 |
Migrate estimates the effective population
sizes and migration rates of n constant populations using
nonrecombining sequence, microsatellite or enzyme electrophoretic data. |
| Modeller |
7v7 |
A program for comparative protein structure
modelling by satisfaction of spatial restraints. |
| Modeltest |
3.7 |
Modeltest helps a user to choose the model of
DNA substitution that best fits the data, among 56 possible models.
Model selection is performed using many processors on the Beowulf
Clusters. |
| Molphy |
2.3b3 |
MOLPHY is a program package for MOLecular
PHYlogenetics. |
| MrBayes |
3.1.1 |
MrBayes is a program for the Bayesian
estimation of phylogeny. We are experimenting with high-speed MrBayes
analyses - parallel versions on the Beowulf Clusters may or may not be
available. MACBLASTER.MBL.EDU (an Apple G5) performs very well. If you
have many analyses to perform, we request you restrict your analysis to
the Beowulf Clusters, even if they are running in single-processor mode
at the moment. Intense MrBayes users should contact
biocomp@lists.mbl.edu for training on use of the HP Alpha HPSRV.MBL.EDU. |
| MUMmer |
3.11 |
A system for aligning whole genome sequences. |
| MUSCLE |
developer version |
Advanced multiple protien sequence alignment
software. |
| NAMOT |
2 |
Nucleic acid molecule modeling tool. |
| Paml |
3.13d |
Phylogenetic Analysis by Maximum Likelihood
(PAML) |
| Paup |
4.0b10 |
PAUP is one of the most widely used software
packages for the inference of evolutionary trees. PAUP may be installed
on a number of computers, but due to the computational intensity of
these searches, large PAUP analyses are only tolerated on the Beowulf
Clusters, where several types of analyses can be performed using
multiple processors. |
| Phrap |
0.990329 |
Phrap is a program for assembling shotgun DNA
sequence data. A number of pipelines are available for running the
complete PHRED, CROSS_MATCH, and PHRAP family of programs. Contact
biocomp@lists.mbl.edu for details. |
| Phred |
|
Phred reads DNA sequencer trace data, calls
bases, assigns quality values to the bases, and writes the base calls
and quality values to output files. |
| Phylip |
3.5c |
PHYLIP is a free package of programs for
inferring phylogenies. Large analyses are only tolerated on the Beowulf
Clusters, where use of multiple processors is in development. |
| Polyphred |
4.22 |
PolyPhred is a program that compares
fluorescence-based sequences across traces obtained from different
individuals to identify heterozygous sites for single nucleotide
substitutions. |
| Primer3 |
|
Primer3 picks primers for PCR reactions. |
| Probcons |
1.1 |
PROBCONS is an efficient protein multiple
sequence alignment program, which has demonstrated a statistically
significant improvement in accuracy compared to several leading
alignment tools.
|
| Pseq-gen |
1.1 |
Protein Sequence-Generator: An application for
the Monte Carlo simulation of protein sequence evolution along
phylogenetic trees. |
| Psi-Phi |
|
Psi-Fi is a suite of programs designed to identify
pseudogenes (attributable both to misannotation and to non-recognition)
through comparative analyses of related genomes
|
| PSORT
2 |
2.0 |
Prediction of subcellular localization of proteins.
|
| PUZZLE |
|
|
| Puzzleboot |
1.03 |
Application of the Roger and Holder puzzleboot
routine to the Beowulf Clusters, with use of multiple processors. |
| Pymol |
0.88 |
PyMOL is a user-sponsored molecular modeling
system with an open-source foundation. |
| R |
1.8.1 |
R is a language and environment for
statistical computing and graphics. |
| R8s |
1.6 |
This is a program for estimating absolute
rates of molecular evolution and divergence times on a phylogenetic
tree. |
| RBSfinder |
|
RBSfinder is a Perl script that implements an
algorithm to find ribosome binding sites for genes in bacterial and
archaeal genomes. |
| Readseq |
|
Readseq takes on the job of guessing what your
input biosequence data format is and converting it to what your
software knows how to handle. |
| ren |
|
Whereas mv can rename (as opposed to move)
only one file at a time, ren can rename many files according to
search and replacement patterns.
|
| RepeatFinder |
|
RepeatFinder is a computational system for
analysis of repetitive structure of genomic sequences. |
| Reputer |
|
The REPuter program family provides state of
the art software solutions to compute and visualize repeats in whole
genomes or chromosomes. |
| Rrtree |
1.1 |
RRTree is a program for relative-rate tests.
It compares substitution rates between DNA or protein sequences grouped
in phylogenetically defined lineages: relative-rate tests with a tree. |
| SAM |
3.4 |
SAM (Sequence Alignment and Modeling) utilizes
hidden markov models (HMMs) to perform sequence similarity searches and
multiple sequence alignments.
|
| SEALS |
0.824 |
SEALS (A System for Easy Analysis of Lots of
Sequences) is a software package of handy sequence and blast report manipulation tools.
SEALS is no longer supported by the author - not all functions may
continue to work. |
| Seg |
|
A program for filtering low complexity regions
in amino acid sequences. |
| Seq-gen |
1.2.7 |
An application for the Monte Carlo simulation
of DNA sequence evolution along phylogenetic trees. |
| Sequencher |
4.2 |
An OSX desktop application for sequence
fragment viewing, editing, and assembling. The JBPC has one
keyserver-based license. Email biocomp@lists.mbl.edu for instructions
on obtaining a client and connecting your client to the keyserver. |
| SignalP |
3.0 |
SignalP predicts the presence and location of
signal peptide cleavage sites in amino acid sequences from different
organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and
eukaryotes. The method incorporates a prediction of cleavage sites and
a signal peptide/non-signal peptide prediction based on a combination
of several artificial neural networks and hidden Markov models. Current
limits: 6000 amino acid maximum sequence length, maximum of 2000
sequences per run, maximum of 200,000 total number of residues per run. |
| Sim4 |
|
Alignment of expressed DNA sequence with a
genomic sequence, allowing for introns. |
| SOAP |
1.1 |
Analysis and cleaning of multiple sequence
alignments. |
| SONS |
1.0 |
Shared OTUs and Similarity; SONS uses non-parametric estimators
to estimate similarity between communities based on membership and structure. Because SONS
is directly compatible with output files from DOTUR, it is possible to quickly determine the
fraction of OTUs shared by two communities for any desired distance level.
package. |
| T-Coffee |
1.37 |
T-Coffee is a multiple sequence alignment
package. |
| Ta2ace |
1.4 |
Ta2ace provides a simple way to convert the
output of TIGR assembler to the new ACE format used by Consed, one of
the most widely used assembly editors. |
| TargetP |
1.1 |
TargetP predicts the subcellular location of
eukaryotic protein sequences. The subcellular location assignment is
based on the predicted presence of any of the N-terminal presequences
chloroplast transit peptide (cTP), mitochondrial targeting peptide
(mTP) or secretory pathway signal peptide (SP). Current limits: 4000
amino acid maximum sequence length, maximum of 2000 sequences per run,
maximum of 200,000 total number of residues per run. |
| TIGR Assembler |
2 |
The TIGR Assembler is the classic assembly
tool developed by TIGR to build a consensus sequence from smaller
sequence fragments. |
| TIGR Gene Indices
Software Tools |
|
This package automates clustering and assembly of
a large EST/mRNA dataset. The clustering is performed by a slightly
modified version of NCBI's megablast , and the resulting clusters are
then assembled using CAP3 assembly program. TGICL starts with a large
multi-FASTA file (and an optional peer quality values file) and outputs
the assembly files as produced by CAP3. Vector should be removed by
LUCY, not CROSSMATCH, and input sequence should be in uppercase.
|
| TmHmm |
2.0c |
Prediction of transmembrane helices in proteins |
| tnimage |
3.3.15a |
A scientific image analysis program that
allows you to create, edit, analyze, and produce color prints of
images. It is particularly useful for analyzing images of SDS and
agarose gels and X-ray or MRI images. |
| Traceviewer |
3.0.2 |
TraceViewer is a Java program that allows you
to see, print, and edit DNA sequencing traces. |
| TransTerm |
|
TransTerm is a program that finds
rho-independent transcription terminators in bacterial genomes. |
| TreeClimber |
1.0 |
TreeClimber uses a parsimony-based test statistic to determine
whether the observed difference between the phylogenies of multiple communities are due to an
accumulation of evolutionary variation or some perturbation. |
| Tree-Puzzle (formerly PUZZLE) |
5.1 |
Maximum likelihood analysis for nucleotide,
amino acid, and two-state data. |
| Treeview (Michael Eisen) |
|
|
| Unveil |
1 |
Unveil is an ab initio gene prediction program
based loosely on the VEIL design. |
| Vector NTI |
7.2 |
Desktop sequence analysis and molecular
biology data management software. |
| Vienna RNA package |
1.4 |
RNA secondary structure prediction and
comparison. |
| Weka |
3.4.1 |
Data mining software in Java. |
| Wise |
2.2.0 |
The Wise2 form compares a protein sequence to
a EST or genomic DNA sequence, allowing for introns and frameshifting
errors. High-throughput, parallel use of several of the WISE programs
is provided on the Beowulf Clusters - please submit your large jobs to
the Beowulf Clusters. We maintain updated, local copies of several Pfam
databases. |
| Wu-blast |
2 |
Washington University BLAST (WU-BLAST) version
2.0 is a powerful software package for gene and protein identification,
using sensitive, selective and rapid similarity searches of protein and
nucleotide sequence databases. We maintain updated, local copies of
several blast databases that can be read by WU-BLAST |
