Software Updates

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.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

EMBOSS

integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

FASTA

a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.

BLAST

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

EMBOSS

integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

BLAST

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

R

a free software environment for statistical computing and graphics.

EMBOSS

integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

R

a free software environment for statistical computing and graphics.

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.

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.

R

a free software environment for statistical computing and graphics.

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.

Bowtie 2

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

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.

R

a free software environment for statistical computing and graphics.

ZDOCK

a full rigid-body search of docking orientations between two proteins.

BLAST

(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.

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.

MUSCLE

(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.

ZDOCK

a full rigid-body search of docking orientations between two proteins.

EMBOSS

integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

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.

R

a free software environment for statistical computing and graphics.

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.

R

a free software environment for statistical computing and graphics.

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.

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.

ZDOCK

a full rigid-body search of docking orientations between two proteins.

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.

Bowtie 2

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

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.

Ghostscript

an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.

ZDOCK

a full rigid-body search of docking orientations between two proteins.

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.

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.

R

a free software environment for statistical computing and graphics.

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.

MUSCLE

(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.

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.

Bowtie

an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

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.

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.

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.

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.

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.

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.

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.

AMPS

(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.

Bowtie 2

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

ZDOCK

a full rigid-body search of docking orientations between two proteins.

WebLogo

command line tools for sequence logo generation.

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.

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.

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.

a2ps

an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages.

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.

bamtools

a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.

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.

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.

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.

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.

Bowtie

an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

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.

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.

ZDOCK

a full rigid-body search of docking orientations between two proteins.

AMPS

(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.

WebLogo

command line tools for sequence logo generation.

edgeR

a Bioconductor software package installed in R 3.2.2 for examining differential expression of replicated count data.

Cufflinks

a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Velvet

a sequence assembler for very short reads.

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.

R

a free software environment for statistical computing and graphics.

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.

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.

Bowtie

an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

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.

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.

a2ps

an Any-to-PostScript filter that processes plain text files, but also pretty prints quite a few popular languages.

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.

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.

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).

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.

bamtools

a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.

Biopython

a set of tools for biological computation written in Python by an international team of developers.

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.

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.

EBSeq

a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.

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.

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.

RSEM

(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.

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.

ZDOCK

a full rigid-body search of docking orientations between two proteins.

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.

maq

(Mapping and Assembly with Qualities) builds mapping assemblies from short reads generated by the next-generation sequencing machines.

Cufflinks

a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

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.

Bowtie

an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

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.

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.

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.

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.

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.

bamtools

a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.

WebLogo

command line tools for sequence logo generation.

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.

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.

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.

edgeR

a Bioconductor software package installed in R 3.2.2 for examining differential expression of replicated count data.

Velvet

a sequence assembler for very short reads.

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.

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.

eXpress

a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

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.

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.

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.

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.

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.

FastQC

a quality control tool for high throughput sequence data.

RSEM

(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.

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.

MACS2

(Model Based Analysis of ChIP-Seq data) a novel algorithm for identifying transcript factor binding sites.

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.

BLAT

(BLAST-Like Alignment Tool) a very fast sequence alignment tool similar to BLAST.

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.

EBSeq

a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.

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.

SPAdes

(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.

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).

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).

HOMER

(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.

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.

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.

Biopython

a set of tools for biological computation written in Python by an international team of developers.

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.

SPAdes

(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.