KING
- Ebuilds: 1, Testing: 2.2.7 Description: Check family relationship and infer population structure
Homepage:https://kingrelatedness.com License: all-rights-reserved
SPAdes
- Ebuilds: 1, Testing: 3.15.5 Description:
truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
dipspades is assembly module for highly polymorphic diploid genomes
Homepage:https://cab.spbu.ru/software/spades License: GPL-2
YASRA
- Ebuilds: 1, Testing: 2.33 Description: Yet Another Short Read Assembler aligning to a reference using LASTZ
Homepage:http://www.bx.psu.edu/miller_lab/ License: GPL-2
aaindex
- Ebuilds: 1, Testing: 9.1-r2 Description:
Amino acid indices and similarity matrices maintained at Kyoto
University. An amino acid index is a set of 20 numerical values
representing any of the different physicochemical and biological
properties of amino acids. The AAindex1 section of the Amino Acid
Index Database is a collection of published indices together with the
result of cluster analysis using the correlation coefficient as the
distance between two indices. This section currently contains 494
indices. Another important feature of amino acids that can be
represented numerically is the similarity between amino acids. Thus, a
similarity matrix, also called a mutation matrix, is a set of 210
numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used
for sequence alignments and similarity searches. The AAindex2 section
of the Amino Acid Index Database is a collection of published amino
acid mutation matrices together with the result of cluster analysis.
This section currently contains 83 matrices.
Homepage:https://www.genome.jp/aaindex/ License: public-domain
abacas
- Ebuilds: 1, Testing: 1.3.1 Description: Order and orientate DNA contigs even via 6-frame protein alignments
Homepage:https://abacas.sourceforge.net License: GPL-2+
afni (ambiguous, available in 2 overlays)
- Ebuilds: 5, Testing: 24.1.16 Description:
Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying
functional MRI data—a technique for mapping human brain activity.
Homepage:http://stnava.github.io/ANTs/ License: GPL-3+
aghermann
- Ebuilds: 1, Testing: 1.1.2-r2 Description:
Aghermann is a program designed around a common workflow in
sleep-research, complete with scoring facility; cairo subpixel
drawing on screen or to file; conventional PSD and EEG Micrcontinuity
profiles; Independent Component Analysis; artifact detection; and
Process S simulation following Achermann et al, 1993.
Homepage:http://johnhommer.com/academic/code/aghermann License: GPL-2+
ants
- Ebuilds: 1, Testing: 2.4.3 Description:
ANTs extracts information from complex datasets that include imaging
(Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing,
interpreting and visualizing multidimensional data. ANTs is popularly
considered a state-of-the-art medical image registration and segmentation
toolkit. ANTsR is an emerging tool supporting standardized multimodality
image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used
medical image processing library to which ANTs developers contribute.
Homepage:https://stnava.github.io/ANTs/ License: BSD
bambus
- Ebuilds: 1, Testing: 2.33-r2 Description: Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.
Homepage:
https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
https://sourceforge.net/projects/amos/files/bambus License: Artistic
bamtools
- Ebuilds: 2, Stable: 2.5.3, Testing: 9999 Description: BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.
Homepage:https://github.com/pezmaster31/bamtools
barrnap
- Ebuilds: 1, Testing: 0.9 Description: Predict Bacterial and Archaeal rRNA genes and output in GFF3 format
Homepage:https://github.com/tseemann/barrnap License: GPL-3
bcftools
- Ebuilds: 4, Testing: 1.23 Description: Utilities for variant calling and manipulating VCF and BCF files
Homepage:http://www.htslib.org License: MIT
bids-schema
- Ebuilds: 2, Testing: 1.7.0_p20220217 Description:
Reference repository for BIDS schema, maintained by under the purview of
BIDS authors. Multiple individual versions are distributed under directory
names corresponding to the versions.
Homepage:https://github.com/bids-standard/bids-schema License: CC-BY-SA-4.0
biobambam2
- Ebuilds: 2, Testing: 2.0.146 Description:
This package contains some tools for processing BAM files including
bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
bamsort: reads BAM and writes BAM resorted by coordinates or query name
bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
Homepage:https://gitlab.com/german.tischler/biobambam2
https://github.com/gt1/biobambam2 License: GPL-3 MIT
biosql
- Ebuilds: 1, Stable: 1.0.1-r2, Testing: 1.0.1-r2 Description: A generic bioinformatics relational database model
Homepage:https://biosql.org/ License: LGPL-3
bismark
- Ebuilds: 1, Testing: 0.23.0 Description:
Bismark is a program to map bisulfite treated sequencing reads to a genome of
interest and perform methylation calls in a single step. The output can be
easily imported into a genome viewer, such as SeqMonk, and enables a researcher
to analyse the methylation levels of their samples straight away. It's main
features are: (1) Bisulfite mapping and methylation calling in one single step;
(2) Supports single-end and paired-end read alignments; (3) Supports ungapped
and gapped alignments; (4) Alignment seed length, number of mismatches etc. are
adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG
and CHH context.
Homepage:https://www.bioinformatics.babraham.ac.uk/projects/ License: GPL-3+
blat
- Ebuilds: 1, Testing: 34-r3 Description: The BLAST-Like Alignment Tool, a fast genomic sequence aligner
Homepage:http://www.cse.ucsc.edu/~kent/ License: blat
brat_bw
- Ebuilds: 1, Testing: 2.0.1 Description: Bisulfite-aware short read mapper, FM-index, no InDel support
Homepage:http://compbio.cs.ucr.edu/brat/ License: GPL-3
brat_nova
- Ebuilds: 1, Testing: 20160103 Description: Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align
Homepage:http://compbio.cs.ucr.edu/brat/ License: GPL-3
brkraw
- Ebuilds: 1, Testing: 0.3.11 Description: Fast and easy statistical learning on NeuroImaging data
Homepage:https://github.com/BrkRaw/brkraw License: GPL-3
bru2nii
- Ebuilds: 1, Testing: 1.0.20180303 Description:
This is a simple tool for converting Bruker ParaVision MRI data to
the NIfTI file format. It includes both a drag-and-drop graphical
interface (Bru2Nii) as well as a command line tool (Bru2).
Homepage:https://github.com/neurolabusc/Bru2Nii License: || ( Artistic GPL-1+ )
bruker2nifti
- Ebuilds: 1, Testing: 1.0.4-r1 Description:
Bruker2nifti is an open source medical image format converter from
raw Bruker ParaVision to NifTi, without any intermediate step through
the DICOM standard format.
Homepage:https://github.com/SebastianoF/bruker2nifti License: MIT
cd-hit
- Ebuilds: 1, Testing: 4.6.6-r1 Description:
CD-HIT is a very widely used program for clustering and comparing large sets
of protein or nucleotide sequences. CD-HIT is very fast and can handle
extremely large databases. CD-HIT helps to significantly reduce the
computational and manual efforts in many sequence analysis tasks and aids in
understanding the data structure and correct the bias within a dataset.
The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D,
CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT
(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a
user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2
datasets and identifies the sequences in db2 that are similar to db1 above
a threshold. CD-HIT-454 is a program to identify natural and artificial
duplicates from pyrosequencing reads. The usage of other programs and
scripts can be found in CD-HIT user's guide.
Homepage:http://weizhong-lab.ucsd.edu/cd-hit/ License: GPL-2
clustal-omega
- Ebuilds: 1, Stable: 1.2.4-r1, Testing: 1.2.4-r1 Description: Scalable multiple alignment of protein sequences
Homepage:http://www.clustal.org/omega/ License: GPL-2
clustalw
- Ebuilds: 2, Stable: 2.1-r2, 1.83-r4, Testing: 2.1-r2 Description: General purpose multiple alignment program for DNA and proteins
Homepage:http://www.clustal.org/ License: GPL-3 LGPL-3
cnrun
- Ebuilds: 1, Testing: 2.1.0-r2 Description:
CNrun is a neuronal network simulator, with these features:
* a conductance- and rate-based Hodgkin-Huxley neurons, a Rall and
Alpha-Beta synapses;
* a 6-5 Runge-Kutta integration method: slow but precise, adjustable;
* Poisson, Van der Pol, Colpitts oscillators and interface for
external stimulation sources;
* NeuroML network topology import/export;
* logging state variables, spikes;
* implemented as a Lua module, for scripting model behaviour (e.g.,
to enable plastic processes regulated by model state);
* interaction (topology push/pull, async connections) with other
cnrun models running elsewhere on a network, with interactions
(planned).
Note that there is no `cnrun' executable, which existed in cnrun-1.*.
Instead, you write a script for your simulation in Lua, and execute
it as detailed in /usr/share/lua-cnrun/examples/example1.lua.
Homepage:http://johnhommer.com/academic/code/cnrun License: GPL-2+
codonw
- Ebuilds: 1, Testing: 1.4.4-r2 Description: Multivariate statistical analysis of codon and amino acid usage
Homepage:https://codonw.sourceforge.net/ License: GPL-2
cutadapt
- Ebuilds: 1, Testing: 4.9 Description: Adapter trimming and other preprocessing of high-throughput sequencing reads
Homepage:https://github.com/marcelm/cutadapt/ License: MIT
cutg
- Ebuilds: 1, Testing: 160-r1 Description:
Codon usage tables maintained at the Kazusa DNA Research Institute.
Codon usage in individual genes has been calculated using the
nucleotide sequence data obtained from the GenBank Genetic Sequence
Database. The compilation of codon usage is synchronized with each
major release of GenBank.
Homepage:http://www.kazusa.or.jp/codon/ License: public-domain
dargcc_bidsdata
- Ebuilds: 1, Testing: 1.0 Description:
BIDS data selection encompassing the wildtype mouse group form the
"Dysfunctional Autism Risk Genes Cause Circuit-Specific Connectivity
Deficits With Distinct Developmental Trajectories" publication, with
DOI: 10.1093/cercor/bhy046 .
Homepage:https://academic.oup.com/cercor/article/28/7/2495/4975475 License: GPL-3
dcm2niix
- Ebuilds: 1, Testing: 1.0.20210317 Description:
dcm2niix is a designed to convert neuroimaging data from the DICOM
format to the NIfTI format. ICOM provides many ways to store/compress
image data, known as transfer syntaxes.
Homepage:https://github.com/rordenlab/dcm2niix License: BSD
dipy
- Ebuilds: 1, Testing: 1.1.1-r1 Description:
Dipy is a free and open source software project for computational neuroanatomy, focusing mainly on
diffusion magnetic resonance imaging (dMRI) analysis. It implements a broad range of algorithms for
denoising, registration, reconstruction, tracking, clustering, visualization, and statistical
analysis of MRI data.
Homepage:https://github.com/nipy/dipy License: BSD
drlfom_bidsdata (ambiguous, available in 2 overlays)
- Ebuilds: 2, Testing: 1.1.1 Description:
BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
and first associated with the DRLFOM publication. The data represents
optp-fMRI mouse brain scans with CBV contrast, tracking serotonergic
stimulation over the course of a fluoxetine drinking water treatment.
Homepage:http://www.aic-fmi.ethz.ch/ License: CC-BY-SA-4.0
edena
- Ebuilds: 1, Testing: 3.131028 Description: De novo short read OLC assembler (overlap-layout-consensus)
Homepage:http://www.genomic.ch/edena.php License: GPL-3
elph
- Ebuilds: 1, Testing: 1.0.1-r3 Description:
ELPH is a general-purpose Gibbs sampler for finding motifs in a set of
DNA or protein sequences. The program takes as input a set containing
anywhere from a few dozen to thousands of sequences, and searches
through them for the most common motif, assuming that each sequence
contains one copy of the motif.
Homepage:http://cbcb.umd.edu/software/ELPH/ License: Artistic
embassy
- Ebuilds: 1, Testing: 6.6.0-r3 Description: A meta-package for installing all EMBASSY packages (EMBOSS add-ons)
Homepage:http://emboss.sourceforge.net/embassy/ License: metapackage
emboss
- Ebuilds: 1, Testing: 6.6.0-r4 Description:
EMBOSS is "The European Molecular Biology Open Software Suite".
EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety
of formats and even allows transparent retrieval of sequence data
from the web. Also, as extensive libraries are provided with the
package, it is a platform to allow other scientists to develop and
release software in true open source spirit. EMBOSS also integrates
a range of currently available packages and tools for sequence
analysis into a seamless whole. EMBOSS breaks the historical trend
towards commercial software packages.
License: Apache-2.0 GPL-3+ CC-BY-3.0
flowsim
- Ebuilds: 1, Testing: 0.3.5 Description:
Provides clonesim, a clone simulator that simulates shotgun
genomic clones, and flowsim, that takes the output from clonesim
(or any other Fasta-formatted file) and generates simulated
reads from them mimicing Roche's 454 pyrosequencing technology,
writing output in 454's native SFF format. The flowgram
generation is based on empirical distributions derived from real
data (although analytic distributions are available too, if you
prefer).
The Darcs repository is at <http://malde.org/~ketil/biohaskell/flowsim>.
Homepage:http://biohaskell.org/Applications/FlowSim License: GPL-2
foldingathome
- Ebuilds: 2, Testing: 7.6.21 Description: Folding@Home is a distributed computing project for protein folding
Homepage:https://foldingathome.org/ License: FAH-EULA-2014 FAH-special-permission
freebayes
- Ebuilds: 1, Testing: 1.3.5 Description: Bayesian gen. variant detector to find short polymorphisms
Homepage:https://github.com/ekg/freebayes License: MIT
gmap
- Ebuilds: 1, Testing: 2020.10.27 Description: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Homepage:http://research-pub.gene.com/gmap/ License: gmap
grabix
- Ebuilds: 1
Description: Provide random access to text files BGZF compressed with bgzip
Homepage:https://github.com/arq5x/grabix License: MIT
grappa
- Ebuilds: 1, Testing: 2.0 Description: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
Homepage:https://www.cs.unm.edu/~moret/GRAPPA/ License: GPL-2
hexamer
- Ebuilds: 1, Testing: 19990330 Description: Predict CDS using 6mers without deriving information from base composition
Homepage:http://www.sanger.ac.uk/resources/software License: all-rights-reserved
irsabi_bidsdata
- Ebuilds: 1, Testing: 1.4 Description:
BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
and first associated with the IRSABI publication. The data represents
f/MRI mouse brain scans with both BOLD and CBV contrasts, and acquired
during optogenetic stimulation over multiple sessions including acute
(i.v.) and chronic (s.c.) fluoxetine administration sessions.
Homepage:https://chymera.eu/docs/focus/open-science/ License: CC-BY-SA-4.0
irsabi_brudata
- Ebuilds: 1, Testing: 1.4.1 Description:
Bruker ParaVision raw data recorded at the ETH/UZH Animal Imaging
Center and first associated with the IRSABI publication. The data
represents f/MRI mouse brain scans with both BOLD and CBV contrasts,
and acquired during optogenetic stimulation over multiple sessions
including acute (i.v.) and chronic (s.c.) fluoxetine administration
sessions.
Homepage:http://www.aic-fmi.ethz.ch/ License: CC-BY-SA-4.0
lastz
- Ebuilds: 1, Testing: 1.04.03 Description: A pairwise DNA sequence aligner, a BLASTZ replacement
Homepage:http://www.bx.psu.edu/~rsharris/lastz/ License: all-rights-reserved
lemur-brain-atlas
- Ebuilds: 1, Testing: 0.1 Description:
MRI template and 120-region atlas for the mouse lemur primate Microcebus
murinus. Generated from 34 animals aged 15-58 months old scanned at 7T
using a T2-weighted sequence, resolution 115 × 115 × 230 µm. The template
was up-sampled to 91 µm isotropic for hand-segmentation of structures,
and also used to create probability maps of grey matter, white matter and
cerebro-spinal fluid.
Homepage:https://www.nitrc.org/projects/mouselemuratlas License: CeCILL-2
mmseqs2
- Ebuilds: 1, Testing: 13.0-r1 Description:
MMseqs2 (Many-against-Many sequence searching) is a software suite toi
search and cluster huge protein and nucleotide sequence sets.
MMseqs2 is open source GPL-licensed software implemented in C++.
The software is designed to run on multiple cores and servers
and exhibits very good scalability. MMseqs2 can run 10000 times
faster than BLAST. At 100 times its speed it achieves almost the
same sensitivity. It can perform profile searches with the same
sensitivity as PSI-BLAST at over 400 times its speed.
Homepage:https://github.com/soedinglab/MMseqs2 License: GPL-3
mosaik
- Ebuilds: 1, Testing: 2.2.30 Description: A reference-guided aligner for next-generation sequencing technologies
Homepage:https://github.com/wanpinglee/MOSAIK License: GPL-2
mothur
- Ebuilds: 1, Stable: 1.48.2, Testing: 1.48.2 Description: Suite of algorithms for ecological bioinformatics
Homepage:https://mothur.org/ License: GPL-3
mrbayes
- Ebuilds: 2, Testing: 3.2.7 Description:
MrBayes is a program for the Bayesian estimation of phylogeny.
Bayesian inference of phylogeny is based upon a quantity called the
posterior probability distribution of trees, which is the probability of a
tree conditioned on the observations. The conditioning is accomplished using
Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
Homepage:https://nbisweden.github.io/MrBayes/ License: GPL-2
mreps
- Ebuilds: 1, Testing: 2.6.01 Description: Identification of serial/tandem repeats in DNA sequences
Homepage:https://mreps.univ-mlv.fr/ License: GPL-2
msautil
- Ebuilds: 1, Testing: 1.1-r1 Description: Reformat/edit FASTA files and compute simple statistics (N50, quartiles, mode)
Homepage:http://bioresearch.byu.edu/msa License: all-rights-reserved
multiqc
- Ebuilds: 1, Testing: 1.33 Description: Aggregate bioinformatics results across many samples into a single report
Homepage:https://multiqc.info/ License: GPL-3
nilearn
- Ebuilds: 1, Testing: 0.9.1-r1 Description:
Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.
It leverages the scikit-learn Python toolbox for multivariate statistics with applications
such as predictive modelling, classification, decoding, or connectivity analysis.
Homepage:http://nilearn.github.io/ License: BSD
nitime
- Ebuilds: 2, Testing: 0.10.2 Description:
Nitime is a library for time-series analysis of data from neuroscience experiments
in both the time and spectral domains.
Homepage:http://nipy.org/nitime/index.html License: BSD
ntCard
- Ebuilds: 2, Testing: 1.2.2 Description: Estimate k-mer coverage histogram of genomics data
Homepage:https://github.com/bcgsc/ntCard License: MIT
nvcz_data
- Ebuilds: 1, Testing: 0.2 Description:
Bruker raw data and BIDS data (recomputed from AFNI HEAD/BRIK files)
from mouse fMRI and optical recordings during hindpaw stimulation.
Homepage:https://gitlab.com/Chymera/nvcz License: GPL-3
nxtrim
- Ebuilds: 1, Testing: 0.4.3 Description: Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker
Homepage:https://github.com/sequencing/NxTrim License: BSD-2
open-ephys-gui
- Ebuilds: 3, Testing: 99999999 Description: Processing, recording, and visualizing multichannel ephys data
Homepage:https://open-ephys.org/gui/ License: GPL-3
opfvta_bidsdata (ambiguous, available in 2 overlays)
- Ebuilds: 2, Testing: 2.1 Description:
BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
and first associated with the OPFVTA publication. The data represents
f/MRI mouse brain scans with both BOLD and CBV contrasts, using block
and phasic stimulation protocols delivered via a laser to the VTA,
which is rendered sensitive by channelrhodopsin expression under
the dopamine transporter promoter.
Homepage:http://www.aic-fmi.ethz.ch/ License: CC-BY-SA-4.0
opfvta_brudata
- Ebuilds: 1, Testing: 2.0 Description:
Raw ParaVision (Bruker vendor acquisition system) MRI data recorded at
the ETH/UZH Animal Imaging Center and first associated with the OPFVTA
publication. The data represents f/MRI mouse brain scans with both
BOLD and CBV contrasts, using block and phasic stimulation protocols
delivered via a laser to the VTA, which is rendered sensitive by
channelrhodopsin expression under the dopamine transporter promoter.
Homepage:http://www.aic-fmi.ethz.ch/ License: CC-BY-SA-4.0
phyml
- Ebuilds: 1, Stable: 2.4.5-r4, Testing: 2.4.5-r4 Description:
Phyml is a simple, fast, and accurate algorithm to estimate large
phylogenies by maximum likelihood. Given input sequence files, it
estimates phylogenies using maximum likelihood, and is capable of
processing large amounts of phylogenetic data.
Homepage:http://atgc.lirmm.fr/phyml/ License: GPL-2
piler
- Ebuilds: 1, Stable: 1.0-r2, Testing: 1.0-r2 Description: Analysis of repetitive DNA found in genome sequences
Homepage:http://www.drive5.com/piler/ License: public-domain
plamri_brudata
- Ebuilds: 1, Testing: 0.1 Description:
Bruker Paravision data archive containing plate scans with T1 and
T2-weighted sequences, as required for testing the PlaMRI package.
Homepage:http://jasanofflab.mit.edu/ License: CC-BY-SA-4.0
primer3
- Ebuilds: 1, Testing: 2.3.7-r1 Description:
Primer3 picks primers for PCR reactions, considering: oligonucleotide
melting temperature, size, GC content, and primer-dimer possibilities;
PCR product size; positional constraints within the source sequence;
and miscellaneous other constraints. All of these criteria are
user-specifiable as constraints, and some are specifiable as terms in
an objective function that characterizes an optimal primer pair.
Homepage:http://primer3.sourceforge.net/ License: GPL-2
prinseq-lite
- Ebuilds: 1, Testing: 0.20.4 Description: Describe, trim, reformat and convert to or form FASTA/FASTQ files
Homepage:http://prinseq.sourceforge.net/ License: GPL-3+
prints
- Ebuilds: 1, Testing: 39.0-r2 Description:
A protein motif fingerprint database maintained at the University of
Manchester. A fingerprint is a group of conserved motifs used to
characterise a protein family; its diagnostic power is refined by
iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs
do not overlap, but are separated along a sequence, though they may be
contiguous in 3D-space. Fingerprints can encode protein folds and
functionalities more flexibly and powerfully than can single motifs,
full diagnostic potency deriving from the mutual context provided by
motif neighbours.
Homepage:http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ License: public-domain
proda
- Ebuilds: 1, Testing: 1.0 Description: Multiple alignment of protein sequences with repeated and shuffled elements
Homepage:http://proda.stanford.edu/ License: public-domain
prosite
- Ebuilds: 1, Testing: 2017.02-r1 Description:
A protein families and domains database maintained at the Swiss
Institude for Bioinformatics. It consists of biologically significant
sites, patterns and profiles that help to reliably identify to which
known protein family (if any) a new sequence belongs. PROSITE currently
contains patterns and profiles specific for more than a thousand
protein families or domains. Each of these signatures comes with
documentation providing background information on the structure and
function of these proteins.
Homepage:https://prosite.expasy.org/ License: swiss-prot
quicktree
- Ebuilds: 1, Testing: 2.5 Description: Rapid reconstruction of phylogenies by the Neighbor-Joining method
Homepage:https://github.com/khowe/quicktree/ License: Apache-2.0
rat-brain-templates
- Ebuilds: 1, Testing: 0.2 Description:
Digital rat brain template collection containing data files in NIfTI
format oriented in the standard RAS space, with origin at bregma for
use in magnetic resonance rat brain imaging.
Homepage:https://gitlab.com/FOS-FMI/rat-brain-templates_generator License: fairuse
raxml
- Ebuilds: 1, Testing: 8.2.13 Description: Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
Homepage:https://github.com/stamatak/standard-RAxML License: GPL-2
rebase
- Ebuilds: 1, Testing: 1901-r2 Description:
The Restriction Enzyme data BASE is a collection of information about
restriction enzymes and related proteins. It is maintained by New
England Biolabs. It contains published and unpublished references,
recognition and cleavage sites, isoschizomers, commercial availability,
methylation sensitivity, crystal and sequence data. DNA
methyltransferases, homing endonucleases, nicking enzymes, specificity
subunits and control proteins are also included. More recently,
putative DNA methyltransferases and restriction enzymes, as predicted
from analysis of genomic sequences, are also listed.
Homepage:http://rebase.neb.com License: public-domain
samri
- Ebuilds: 3, Testing: 9999 Description:
SAMRI provides fMRI preprocessing, metadata parsing, and data analysis functions
and pipelines. SAMRI integrates functionalities from a number of other packages
to create higher-level tools.
Homepage:https://github.com/IBT-FMI/SAMRI
seaview
- Ebuilds: 1, Testing: 4.6-r2 Description:
SeaView is a graphical multiple sequence alignment editor developped by
Manolo Gouy. SeaView is able to read and write various alignment
formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to
manually edit the alignment, and also to run DOT-PLOT or CLUSTALW
programs to locally improve the alignment.
Homepage:http://pbil.univ-lyon1.fr/software/seaview.html License: public-domain
sim4
- Ebuilds: 1, Testing: 20030921-r2 Description:
sim4 is a similarity-based tool for aligning an expressed DNA sequence
(EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects
end matches when the two input sequences overlap at one end (i.e., the
start of one sequence overlaps the end of the other).sim4 employs a
blast-based technique to first determine the basic matching blocks
representing the "exon cores". In this first stage, it detects all
possible exact matches of W-mers (i.e., DNA words of size W) between
the two sequences and extends them to maximal scoring gap-free
segments. In the second stage, the exon cores are extended into the
adjacent as-yet-unmatched fragments using greedy alignment algorithms,
and heuristics are used to favor configurations that conform to the
splice-site recognition signals (GT-AG, CT-AC). If necessary, the
process is repeated with less stringent parameters on the unmatched
fragments.
Homepage:http://globin.cse.psu.edu/html/docs/sim4.html License: GPL-2
snapgene
- Ebuilds: 2, Testing: 8.2.2 Description: Software for plasmid mapping, primer design, and restriction site analysis
Homepage:https://www.snapgene.com/snapgene-viewer License: snapgene
spm
- Ebuilds: 1, Testing: 12_p7771 Description: Analysis of brain imaging data sequences for Octave or Matlab
Homepage:https://www.fil.ion.ucl.ac.uk/spm/ License: GPL-2+
t-coffee
- Ebuilds: 1, Testing: 11.00-r3 Description:
T-Coffee is a multiple sequence alignment package. Given a set of
sequences (Proteins or DNA), T-Coffee generates a multiple sequence
alignment. Version 2.00 and higher can mix sequences and structures.
T-Coffee allows the combination of a collection of multiple/pairwise,
global or local alignments into a single model. It also allows to
estimate the level of consistency of each position within the new
alignment with the rest of the alignments.
Homepage:http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html License: GPL-2
tree-puzzle
- Ebuilds: 1, Testing: 5.2-r1 Description:
TREE-PUZZLE is a computer program to reconstruct phylogenetic trees
from molecular sequence data by maximum likelihood. It implements a
fast tree search algorithm, quartet puzzling, that allows analysis of
large data sets and automatically assigns estimations of support to
each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified
trees. Branch lengths can be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment. TREE-PUZZLE also conducts a number of statistical
tests on the data set (chi-square test for homogeneity of base
composition, likelihood ratio clock test, Kishino-Hasegawa test). The
models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for
nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids,
and F81 for two-state data. Rate heterogeneity is modeled by a discrete
Gamma distribution and by allowing invariable sites. The corresponding
parameters can be inferred from the data set.
Homepage:http://www.tree-puzzle.de License: GPL-2
treeviewx
- Ebuilds: 1, Stable: 0.5.1.20100823_p4-r1, Testing: 0.5.1.20100823_p4-r1 Description:
TreeView X is a program for displaying phylogenetic trees on Linux and
UNIX platforms. It can read and display NEXUS and Newick format tree
files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other
programs).
Homepage:https://github.com/rdmpage/treeviewx License: GPL-2
trnascan-se
- Ebuilds: 1, Testing: 1.31-r3 Description:
tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA
genes, with a false positive rate of less than one per 15 gigabases,
and with a search speed of about 30 kb/second. It was implemented for
large-scale human genome sequence analysis, but is applicable to
other DNAs as well.
Homepage:http://lowelab.ucsc.edu/tRNAscan-SE/ License: GPL-2
uchime
- Ebuilds: 1, Stable: 4.2.40-r1, Testing: 4.2.40-r1 Description:
UCHIME is a new algorithm for detecting chimeric sequences. It was developed in
collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob
Knight. Chimeras are commonly created during DNA sample amplification by
PCR, especially in community sequencing experiments using single regions
such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can
detect chimeras using a reference database or de novo using abundance
information on the assumption that chimeras are less abundant than their
parents because they must have undergone fewer rounds of amplification.
Homepage:https://www.drive5.com/usearch/manual/uchime_algo.html License: public-domain
ucsc-genome-browser
- Ebuilds: 1, Testing: 260-r2 Description: The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath
Homepage:http://genome.ucsc.edu/ License: blat
ztau_bidsdata
- Ebuilds: 1, Testing: 1.0 Description:
BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
and first associated with the ZTAU study. The archive contains
longitudinal f/MRI mouse brain scans using both T2 and T2* (BOLD)
contrasts. Functional data is acquired during anesthetized resting
state.
Homepage:http://www.aic-fmi.ethz.ch/ License: CC-BY-SA-4.0