Jun 13 2016
|
DIAMOND
a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
Updated versions:
0.7.12 | Linux 64
|
Jun 03 2016
|
FASTA
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
Updated versions:
36.3.8d | OS X INTEL
36.3.8d | Linux 64
36.3.8c | Linux 64
|
Jun 03 2016
|
EMBOSS
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Updated versions:
6.5.7 | OS X INTEL
|
Jun 03 2016
|
FASTA
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
Updated versions:
36.3.8b | Linux 64
|
Jun 03 2016
|
BLAST
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
Updated versions:
2.2.26 | OS X INTEL
|
Jun 03 2016
|
EMBOSS
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Updated versions:
6.5.7 | Linux 64
|
Jun 03 2016
|
BLAST
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
Updated versions:
2.2.26 | Linux 64
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
3.2.2 | Linux 64
|
Jun 03 2016
|
EMBOSS
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Updated versions:
6.4.0 | Linux 64
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
3.2.2 | OS X INTEL
|
Jun 03 2016
|
ImageJ
a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.
Updated versions:
1.49 | Linux 64
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
3.2.1 | OS X INTEL
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
3.2.1 | OS X INTEL
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
3.2.1 | Linux 32
|
Jun 03 2016
|
Bowtie 2
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Updated versions:
2.2.9 | Linux 64
|
Jun 03 2016
|
BLAST+
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
Updated versions:
2.3.0 | Linux 64
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
3.2.0 | Linux 64
3.0.3 | OS X INTEL
|
Jun 03 2016
|
ZDOCK
a full rigid-body search of docking orientations between two proteins.
Updated versions:
3.0.2 | Linux 64
|
Jun 03 2016
|
BLAST
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
Updated versions:
2.2.25 | Linux 64
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
3.2.1 | Linux 64
|
Jun 03 2016
|
MUSCLE
(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.
Updated versions:
3.8.31 | Linux 64
|
Jun 03 2016
|
ZDOCK
a full rigid-body search of docking orientations between two proteins.
Updated versions:
3.0.2 | OS X INTEL
|
Jun 03 2016
|
EMBOSS
integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Updated versions:
6.3.1 | Linux 64
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
3.2 | OS X INTEL
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
3.0.3 | Linux 64
|
Jun 03 2016
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.3.1 | OS X INTEL
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
2.13.0 | Linux 64
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
3.2 | powermac
|
Jun 03 2016
|
Fiji
an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
Updated versions:
20160310 | OS X INTEL
|
Jun 03 2016
|
ZDOCK
a full rigid-body search of docking orientations between two proteins.
Updated versions:
3.0.1 | Linux 32
|
Jun 03 2016
|
cython
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
cython is installed as a module within python.
Updated versions:
0.23.4 | Linux 64
|
Jun 03 2016
|
Bowtie 2
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Updated versions:
2.2.8 | Linux 64
|
Jun 03 2016
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.3.1 | Linux 64
|
Jun 03 2016
|
Ghostscript
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
Updated versions:
9.04 | Linux 64
|
Jun 03 2016
|
ZDOCK
a full rigid-body search of docking orientations between two proteins.
Updated versions:
3.0.1 | OS X INTEL
|
Jun 03 2016
|
breseq
a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.
Updated versions:
1.00rc8 | Linux 64
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
3.2 | Linux 32
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
2.13.0 | OS X INTEL
|
Jun 03 2016
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.3 | OS X INTEL
|
Jun 03 2016
|
MUSCLE
(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.
Updated versions:
3.8.31 | OS X INTEL
|
Jun 03 2016
|
Fiji
an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
Updated versions:
20160310 | Linux 64
|
Jun 03 2016
|
Bowtie
an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
Updated versions:
1.1.2 | OS X INTEL
|
Jun 03 2016
|
NumPy
contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.
NumPy is installed as a module within Python.
Updated versions:
1.9.2 | OS X INTEL
|
Jun 03 2016
|
Pysam
a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages.
Pysam is installed as a module within python.
Updated versions:
0.8.3 | OS X INTEL
|
Jun 03 2016
|
pandas
a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
pandas is installed as a module within python.
Updated versions:
0.16.2 | Linux 64
|
Jun 03 2016
|
cython
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
cython is installed as a module within python.
Updated versions:
0.23.4 | OS X INTEL
|
Jun 03 2016
|
BCFtools
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:
1.3.1 | Linux 64
|
Jun 03 2016
|
Perl
is a highly capable, feature-rich programming language with over 30 years of development. Perl runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
Updated versions:
5.10.1 | OS X INTEL
|
Jun 03 2016
|
TopHat
a fast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Updated versions:
2.1.1 | OS X INTEL
|
Jun 03 2016
|
AMPS
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
Updated versions:
2.3a | Linux 64
|
Jun 03 2016
|
Bowtie 2
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Updated versions:
2.2.7 | Linux 64
|
Jun 03 2016
|
ZDOCK
a full rigid-body search of docking orientations between two proteins.
Updated versions:
3.0 | Linux 64
|
Jun 03 2016
|
WebLogo
command line tools for sequence logo generation.
Updated versions:
3.4 | OS X INTEL
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
2.61 | OS X INTEL
|
Jun 03 2016
|
RStudio
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Updated versions:
0.99.491 | Linux 64
|
Jun 03 2016
|
DIAMOND
a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
Updated versions:
0.7.9 | Linux 64
|
Jun 03 2016
|
a2ps
an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages.
Updated versions:
4.14 | OS X INTEL
|
Jun 03 2016
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.3 | Linux 64
|
Jun 03 2016
|
bamtools
a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
Updated versions:
2.4.0 | OS X INTEL
|
Jun 03 2016
|
pandas
a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
pandas is installed as a module within python.
Updated versions:
0.16.2 | OS X INTEL
|
Jun 03 2016
|
BCFtools
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:
1.3.1 | OS X INTEL
|
Jun 03 2016
|
NumPy
contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.
NumPy is installed as a module within Python.
Updated versions:
1.9.2 | Linux 64
|
Jun 03 2016
|
Pysam
a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages.
Pysam is installed as a module within python.
Updated versions:
0.9.1.4 | Linux 64
|
Jun 03 2016
|
Bowtie
an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
Updated versions:
1.1.2 | Linux 64
|
Jun 03 2016
|
GATK
(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Updated versions:
3.4-46 | Linux 64
|
Jun 03 2016
|
cython
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
cython is installed as a module within python.
Updated versions:
0.23 | OS X INTEL
|
Jun 03 2016
|
ZDOCK
a full rigid-body search of docking orientations between two proteins.
Updated versions:
3.0 | OS X INTEL
|
Jun 03 2016
|
AMPS
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
Updated versions:
2.3a | OS X INTEL
|
Jun 03 2016
|
WebLogo
command line tools for sequence logo generation.
Updated versions:
3.4 | Linux 64
|
Jun 03 2016
|
edgeR
a Bioconductor software package installed in R 3.2.2 for examining differential expression of replicated count data.
Updated versions:
3.12.0 | OS X INTEL
|
Jun 03 2016
|
Cufflinks
a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Updated versions:
2.1.1 | OS X INTEL
|
Jun 03 2016
|
Velvet
a sequence assembler for very short reads.
Updated versions:
1.2.10-kmer155 | Linux 64
|
Jun 03 2016
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
0.1.19 | OS X INTEL
|
Jun 03 2016
|
R
a free software environment for statistical computing and graphics.
Updated versions:
2.11.1 | OS X INTEL
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
2.61 | Linux 32
|
Jun 03 2016
|
TopHat
a fast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Updated versions:
2.1.1 | Linux 64
|
Jun 03 2016
|
Bowtie
an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
Updated versions:
1.0.0 | OS X INTEL
|
Jun 03 2016
|
Perl
is a highly capable, feature-rich programming language with over 30 years of development. Perl runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
Updated versions:
5.10.1 | Linux 64
|
Jun 03 2016
|
Trinity
a software package comprised of three independent software modules (Inchworm, Chrysalis, and Butterfly) for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Updated versions:
r20140717 | Linux 64
|
Jun 03 2016
|
a2ps
an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages.
Updated versions:
4.14 | Linux 64
|
Jun 03 2016
|
BCFtools
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:
1.3 | OS X INTEL
|
Jun 03 2016
|
Cytoscape
a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Updated versions:
3.2.1 | Linux 64
|
Jun 03 2016
|
pytz
cross platform time zone library that brings the Olson tz database into Python and allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo).
Updated versions:
2016.6.1 | OS X INTEL
|
Jun 03 2016
|
HISAT2
(Hierarchical Indexing for Spliced Alignment of Transcripts) a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). HISAT2 is a successor to both HISAT and TopHat2.
Updated versions:
2.0.1-beta | OS X INTEL
|
Jun 03 2016
|
bamtools
a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
Updated versions:
2.4.0 | Linux 64
|
Jun 03 2016
|
Biopython
a set of tools for biological computation written in Python by an international team of developers.
Updated versions:
1.54 | Linux 64
|
Jun 03 2016
|
DESeq2
a Bioconductor software package installed in R 3.2.2 that estimates variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Updated versions:
1.10.0 | OS X INTEL
|
Jun 03 2016
|
BWA
(Burrows-Wheeler Aligner) a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
Updated versions:
0.7.7-r441 | OS X INTEL
|
Jun 03 2016
|
EBSeq
a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.
Updated versions:
1.10.0 | OS X INTEL
|
Jun 03 2016
|
RStudio
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Updated versions:
0.99.473 | Linux 64
|
Jun 03 2016
|
ABySS
a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
Updated versions:
1.9.0 | OS X INTEL
|
Jun 03 2016
|
RSEM
(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.
Updated versions:
1.2.25 | OS X INTEL
|
Jun 03 2016
|
TopHat
a fast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Updated versions:
2.0.11 | Linux 64
|
Jun 03 2016
|
ZDOCK
a full rigid-body search of docking orientations between two proteins.
Updated versions:
3.0 | Linux 32
|
Jun 03 2016
|
cython
an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
cython is installed as a module within python.
Updated versions:
0.20.2 | Linux 64
|
Jun 03 2016
|
maq
(Mapping and Assembly with Qualities) builds mapping assemblies from short reads generated by the next-generation sequencing machines.
Updated versions:
0.7.1 | Linux 64
|
Jun 03 2016
|
Cufflinks
a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Updated versions:
2.1.1 | Linux 64
|
Jun 03 2016
|
I-TASSER
(Iterative Threading ASSEmbly Refinement) a hierarchical approach to protein structure and function prediction. Structural templates are first identified from the PDB by multiple threading approach LOMETS; full-length atomic models are then constructed by iterative template fragment assembly simulations. Finally, function inslights of the target are derived by threading the 3D models through protein function database BioLiP.
Updated versions:
4.4 | Linux 64
|
Jun 03 2016
|
Bowtie
an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
Updated versions:
1.0.0 | Linux 64
|
Jun 03 2016
|
MEME Suite
(Multiple EM for Motif Elicitation) a collection of motif-based sequence analysis tools for discovering motifs in a group of related DNA or protein sequences.
Updated versions:
4.10.1 | Linux 64
|
Jun 03 2016
|
seqLogo
a Bioconductor software package installed in R 3.2.2 that takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo.
Updated versions:
3.1 | Linux 64
|
Jun 03 2016
|
Clustal Omega
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
Updated versions:
1.2.1 | Linux 64
|
Jun 03 2016
|
FastQ Screen
allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
Updated versions:
0.5.1 | Linux 64
|
Jun 03 2016
|
BCFtools
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:
1.3 | Linux 64
|
Jun 03 2016
|
bamtools
a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
Updated versions:
2.3.0 | Linux 64
|
Jun 03 2016
|
WebLogo
command line tools for sequence logo generation.
Updated versions:
2.8.2 | Linux 64
|
Jun 03 2016
|
YAP
an extensible parallel framework, written in Python using OpenMPI libraries that allows researchers to quickly build high throughput big data pipelines without extensive knowledge of parallel programming.
Updated versions:
1.0 | Linux 64
|
Jun 03 2016
|
GATK
(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Updated versions:
3.1-1 | Linux 64
|
Jun 03 2016
|
VCFtools
a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project.
Updated versions:
0.1.12b | Linux 64
|
Jun 03 2016
|
edgeR
a Bioconductor software package installed in R 3.2.2 for examining differential expression of replicated count data.
Updated versions:
3.12.0 | Linux 64
|
Jun 03 2016
|
Velvet
a sequence assembler for very short reads.
Updated versions:
1.2.10 | Linux 64
|
Jun 03 2016
|
PSIPRED
uses a simple and accurate secondary structure prediction method incorporating two feed-forward neural networks which perform an analysis on output obtained from BLAST.
Updated versions:
2.61 | powermac
|
Jun 03 2016
|
VelvetOptimiser
a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
Updated versions:
2.2.5 | Linux 64
|
Jun 03 2016
|
eXpress
a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
Updated versions:
1.5.1 | Linux 64
|
Jun 03 2016
|
BETA
(Binding and Expression Target Analysis) a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
Updated versions:
1.0.7 | Linux 64
|
Jun 03 2016
|
BWA
(Burrows-Wheeler Aligner) a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
Updated versions:
0.7.7-r441 | Linux 64
|
Jun 03 2016
|
RStudio
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Updated versions:
0.99.473 | OS X INTEL
|
Jun 03 2016
|
ABySS
a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
Updated versions:
1.9.0 | Linux 64
|
Jun 03 2016
|
SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
0.1.19 | Linux 64
|
Jun 03 2016
|
FastQC
a quality control tool for high throughput sequence data.
Updated versions:
0.11.2 | Linux 64
|
Jun 03 2016
|
RSEM
(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.
Updated versions:
1.2.25 | Linux 64
|
Jun 03 2016
|
breseq
a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.
Updated versions:
0.27.1 | Linux 64
|
Jun 03 2016
|
MACS2
(Model Based Analysis of ChIP-Seq data) a novel algorithm for identifying transcript factor binding sites.
Updated versions:
2.1.0 | Linux 64
|
Jun 03 2016
|
DESeq2
a Bioconductor software package installed in R 3.2.2 that estimates variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Updated versions:
1.10.0 | Linux 64
|
Jun 03 2016
|
BLAT
(BLAST-Like Alignment Tool) a very fast sequence alignment tool similar to BLAST.
Updated versions:
36 | Linux 64
|
Jun 03 2016
|
MISO
(Mixture-of-Isoforms) for isoform quantitation using RNA-Seq is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.
MISO is installed as a standalone program and as a module within python.
Updated versions:
0.5.2 | Linux 64
|
Jun 03 2016
|
EBSeq
a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.
Updated versions:
1.10.0 | Linux 64
|
Jun 03 2016
|
Pysam
a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages.
Pysam is installed as a module within python.
Updated versions:
0.8.3 | Linux 64
|
Jun 03 2016
|
SPAdes
(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.
Updated versions:
3.7.1 | Linux 64
|
Jun 03 2016
|
pytz
cross platform time zone library that brings the Olson tz database into Python and allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo).
Updated versions:
2016.6.1 | Linux 64
|
Jun 03 2016
|
BIANA
a biological database integration and network management framework written in Python that uses a high level abstraction schema to define databases providing any kind of biological information (both individual entries and their relationships).
Updated versions:
1.3.1 | Linux 64
|
Jun 03 2016
|
HOMER
(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
Updated versions:
4.7 | Linux 64
|
Jun 03 2016
|
HISAT2
(Hierarchical Indexing for Spliced Alignment of Transcripts) a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). HISAT2 is a successor to both HISAT and TopHat2.
Updated versions:
2.0.1-beta | Linux 64
|
Jun 03 2016
|
Trinity
a software package comprised of three independent software modules (Inchworm, Chrysalis, and Butterfly) for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Updated versions:
2.0.2 | Linux 64
|
Jun 03 2016
|
Biopython
a set of tools for biological computation written in Python by an international team of developers.
Updated versions:
1.54 | OS X INTEL
|
Jun 03 2016
|
DIAMOND
a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
Updated versions:
0.7.11 | Linux 64
|
Jun 02 2016
|
SPAdes
(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.
Updated versions:
3.7.1-kmer256 | Linux 64
3.9.0-kmer256 | Linux 64
|