Debian Med Cloud packages

ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread.

Este paquete recoge todas esas más bien pequeñas aplicaciones que acedb recoge bajo el objetivo 'other' de su Makefile.

efetch: presuntamente la abreviatura de 'entry fetch', recoge información de bases de datos sobre secuencias de ADN y proteínas comunes.

Aevol is a digital genetics model: populations of digital organisms are subjected to a process of selection and variation, which creates a Darwinian dynamics.

By modifying the characteristics of selection (e.g. population size, type of environment, environmental variations) or variation (e.g. mutation rates, chromosomal rearrangement rates, types of rearrangements, horizontal transfer), one can study experimentally the impact of these parameters on the structure of the evolved organisms. In particular, since Aevol integrates a precise and realistic model of the genome, it allows for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).

The simulation platform comes along with a set of tools for analysing phylogenies and measuring many characteristics of the organisms and populations along evolution.

Alien_hunter es una aplicación para la predicción de posibles eventos de Transferencia Horizontal de Genes (HGT) con la implementación de Motivos de Orden Variable Interpolados (IVOMs). Un enfoque IVOM explota sesgos composicionales usando distribuciones de motivo de orden variable y capturas más fiables en comparación con la composición local de una secuencia métodos de orden fijo. Opcionalmente las predicciones pueden ser analizadas en un modelo de Hidden Markov de segundo orden de dos estados (HMM), en la detección de un punto de cambio marco, para optimizar la localización de los límites de las regiones previstas. Las predicciones (formato embl) se pueden cargar automáticamente en el visor de genoma de Artemis disponible libremente en: http://www.Sanger.AC.uk/software/Artemis/.

ALTree was designed to perform association detection and localization of susceptibility sites using haplotype phylogenetic trees: first, it allows the detection of an association between a candidate gene and a disease, and second, it enables to make hypothesis about the susceptibility loci.

AMAP is a command line tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation.

The Java visualisation tool of AMAP 2.2 is not yet packaged in Debian.

AmpliconNoise is a package of applications to clean up high-throughput sequence data. It consists of three main parts:

Pyronoise - does flowgram-based clustering to spot misreads SeqNoise - removes PCR point mutations Perseus - removes PCR chimeras without the need for a set of reference sequences

Previously there was a standalone "Pyronoise" by the same authors and this package includes an updated version. There is also a "Denoiser" in Qiime which is related but distinct.

Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. It's most useful for the alignment of sequencing reads where the DNA sequence is somehow modified (think ancient DNA or bisulphite treatment) and/or there is more divergence between sample and reference than what fast mappers will handle gracefully (say the reference genome is missing and a related species is used instead).

The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program.

ARDEN (Artificial Reference Driven Estimation of false positives in NGS data) is a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.

Autodock es el principal representante de los programas que tratan la simulación del acoplamiento de pequeños ligamentos químicos en lugar de grandes receptores de la proteína. Las versiones anteriores tenían toda la flexibilidad en los ligamentos, mientras que la proteína se mantuvo más bien rígida. Esta última versión 4 también permite una flexibilidad de cadenas laterales seleccionadas de residuos en la superficie, es decir, tiene en cuenta la rotación.

El programa Autodock realiza el acoplamiento de ligamentos a un conjunto de rejillas que describen el objetivo de la proteína. AutoGrid pre-calcula estas rejillas.

AutoDock Vina is a program to support drug discovery, molecular docking and virtual screening of compound libraries. It offers multi-core capability, high performance and enhanced accuracy and ease of use.

The same institute also developed autodock, which is widely used.

O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461

El AutoDockSuite aborda el análisis molecular del acoplamiento de compuestos químicos más pequeños a sus receptores de conocida estructura tridimensional.

El programa AutoGrid realiza los cálculos previos para el acoplamiento de un ligando a un conjunto de rejilas que describen el efecto que la proteína tiene en cargas puntuales. Entonces el programa AutoDock analiza el efecto de estas fuerzas sobre el ligando.

BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

BamTools provides both a C++ API for BAM file support as well as a command-line toolkit.

This is the bamtools command-line toolkit.

Available bamtools commands:

 convert  Converts between BAM and a number of other formats
 count    Prints number of alignments in BAM file(s)
 coverage Prints coverage statistics from the input BAM file
 filter   Filters BAM file(s) by user-specified criteria
 header   Prints BAM header information
 index    Generates index for BAM file
 merge    Merge multiple BAM files into single file
 random   Select random alignments from existing BAM file(s), intended more
          as a testing tool.
 resolve  Resolves paired-end reads (marking the IsProperPair flag as needed)
 revert   Removes duplicate marks and restores original base qualities
 sort     Sorts the BAM file according to some criteria
 split    Splits a BAM file on user-specified property, creating a new BAM
          output file for each value found
 stats    Prints some basic statistics from input BAM file(s)

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together.

The groupBy utility is distributed in the filo package.

El proyecto Bioperl es un trabajo coordinado para recolectar métodos informáticos usados de forma rutinaria en bioinformática en un conjunto estándar tipo CPAN, bien documentado y con módulos de Perl disponibles libremente. Está muy bien aceptado por la comunidad y se usa en muchos proyectos destacados, p.ej. en Ensembl.

Los paquetes recomendados son necesarios para ejecutar algunos de los binarios incluídos. Para una explicación detallada, incluyendo los módulos de Perl específicos, lea README.Debian.

El paquete sugerido amplía las páginas del manual.

Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.

SQUID es una biblioteca de funciones de código C para el análisis de secuencias. También incluye varios programas pequeños para hacer conversiones, mostrar estadísticas, manipular y hacer otras funciones en archivos de secuencias.

El nombre original del paquete es «squid» pero, dado que ya existe un paquete denominado «squid» en el repositorio (un proxy caché), se ha renombrado como «biosquid».

Este paquete contiene algunas herramientas para mostrar las características de la biblioteca SQUID.

This is a transitional dummy package for ncbi-blast+-legacy. It can safely be removed.

This package addresses the problem to interpret the results from the latest (2010) DNA sequencing technologies. Those will yield fairly short stretches and those cannot be interpreted directly. It is the challenge for tools like Bowtie to give a chromosomal location to the short stretches of DNA sequenced per run.

Bowtie aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes

Boxshade es un programa para crear impresiones de buena apariencia a partir de proteínas de alineación múltiple o secuencias de ADN. El programa no desarrolla el alineamiento por sí mismo y necesita que se le entregue un archivo creado por un programa de alineación múltiple o editado a mano con las herramientas respectivas.

Boxshade lee secuencias de alineación múltiple desde archivos de PILEUP-MSF, CLUSTAL-ALN, datos de MALIGNED y archivos guardados de ESEE (limitado a un máximo de 150 secuencias de hasta 10000 elementos cada una). Se pueden aplicar varios tipos de sombreados a residuos idénticos/similares. La salida se dibuja en pantalla o en un archivo en los formatos: ANSI/VT100, PS/EPS, RTF, HPGL, ReGIS, LJ250-printer, ASCII, xFIG, PICT o HTML.

BWA is 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. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Cassiopee index and search library C implementation. It is a complete rewrite of the ruby Cassiopee gem. It scans an input genomic sequence (dna/rna/protein) and search for a subsequence with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions.

This package contains the cassiopee and cassiopeeknife tools.

cd-hit contains a number of programs designed to quickly group sequences. cd-hit groups proteins into clusters that meet a user-defined similarity threshold. cd-hit-est is similar to cd-hit, but designed to group nucleotide sequences (without introns). cd-hit-est-2d is similar to cd-hit-2d but designed to compare two nucleotide datasets. A number of other related programs are also in this package. Please see the cd-hit user manual, also part of this package, for further information.

CDB (Constant DataBase) can be used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files. It has the option to compress data records in order to save space.

Circos visualiza datos en un plano circular — ideal para explorar relaciones entre objetos o posiciones, y crear gráficos altamente informativos de calidad profesional.

Este paquete proporciona el motor de trazado Circos, que es controlado por línea de órdenes (como gnuplot) y completamente automatizable.

Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.

ClonalFrame identifica las relaciones clonales entre los miembros de una muestra, al mismo tiempo que estima la posición cromosómica de la recombinación homóloga de eventos que han interrumpido la herencia clónica.

ClonalFrame puede aplicarse a cualquier tipo de datos de secuencia, desde un solo fragmento de ADN a los genomas enteros. Es muy adecuado para el análisis de datos MLST, donde 7 fragmentos genómicos han sido secuenciados, pero se vuelve progresivamente más potente cuando las regiones secuenciadas aumentan en longitud y número hasta genomas completos. Sin embargo, requiere que las secuencias estén alineadas. Si tiene información genómica que no está alineada, se recomienda usar Mauve, el cual produce un alineamiento de todos los genomas bacterianos en el formato exacto requerido para el análisis con ClonalFrame.

Clustal Omega is a general-purpose multiple sequence alignment (MSA) program, primarily for amino-acid sequences. It produces high quality MSAs and is capable of handling data sets of hundreds of thousands of sequences in reasonable time, using multiple processors where available.

This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. Clustal W is very well accepted.

The output of Clustal W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM.

ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

ConCavity takes as input a PDB format protein structure and optionally files that characterize the evolutionary sequence conservation of the chains in the structure file.

The following result files are produced by default:

• Residue ligand binding predictions for each chain (*.scores).
• Residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb).
• Pocket prediction locations in a DX format file (*.dx).
• PyMOL script to visualize the predictions (*.pml).

This package provides score_conservation(1), a tool to score protein sequence conservation.

The following conservation scoring methods are implemented:

• sum of pairs
• weighted sum of pairs
• Shannon entropy
• Shannon entropy with property groupings (Mirny and Shakhnovich 1995, Valdar and Thornton 2001)
• relative entropy with property groupings (Williamson 1995)
• von Neumann entropy (Caffrey et al 2004)
• relative entropy (Samudrala and Wang 2006)
• Jensen-Shannon divergence (Capra and Singh 2007)

A window-based extension that incorporates the estimated conservation of sequentially adjacent residues into the score for each column is also given. This window approach can be applied to any of the conservation scoring methods.

The program accepts alignments in the CLUSTAL and FASTA formats.

The sequence-specific output can be used as the conservation input for concavity.

Conservation is highly predictive in identifying catalytic sites and residues near bound ligands.

GNU Datamash es un programa de línea de órdenes que realiza operaciones básicas numéricas, de texto y estadísticas en archivos de datos de entrada de texto. Está diseñado para ser portátil y seguro, y ayuda a los investigadores a automatizar fácilmente los procesos de análisis, sin necesidad de escribir código o incluso scripts cortos.

DIALIGN2 is a command line tool to perform multiple alignment of protein or DNA sequences. It constructs alignments from gapfree pairs of similar segments of the sequences. This scoring scheme for alignments is the basic difference between DIALIGN and other global or local alignment methods. Note that DIALIGN does not employ any kind of gap penalty.

DIALIGN-TX es una aplicación basada en línea de comandos para realizar alineamientos múltiples de proteínas o secuencias de ADN. Es una re-implementación completa del enfoque fundamental que incluye nuevas mejoras y heurísticas que mejoran significativamente la calidad de los alineamientos de la salida, comparado con DIALIGN 2.2 y DIALIGN-T. Para el alineamiento de pares, DIALIGN-TX usa un algoritmo «fragment-chaining» que favorece cadenas de alineamientos locales de baja puntuación frente a los fragmentos aislados de alta puntuación. Para alineamientos múltiples, DIALIGN-TX emplea un procedimiento «greedy» mejorado que es menos sensible a las falsas similitudes entre secuencias locales.

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).

Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.

The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP:

 1) its mean read coverage
 2) the (phred) quality of reads generating the polymorphism.

This program is superseded by DiscoSnp++.

'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Disulfide bridges play a major role in the stabilization of the folding process for several proteins. Prediction of disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. In addition, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks.

'disulfinder' predicts disulfide patterns in two computational stages: (1) the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier; (2) cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern.

dnaclust is a tool for clustering large number of short DNA sequences. The clusters are created in such a way that the "radius" of each clusters is no more than the specified threshold.

The input sequences to be clustered should be in Fasta format. The id of each sequence is based on the first word of the seqeunce in the Fasta format. The first word is the prefix of the header up to the first occurrence of white space characters in the header.

DSSP is an application you use to assign the secondary structure of a protein based on its solved three dimensional (3D) structure.

This version (4.2) of DSSP is a rewrite that writes annotated mmCIF files by default but can still produce the older dssp format. New is also the support of PP helices.

Los programas DOMAINATRIX han sido desarrollados por Jon Ison y sus compañeros en MRC HGMP para su investigación del dominio de las proteínas. Se incluyen como un paquete EMBASSY como un trabajo en curso.

Las aplicaciones que se incluyen en esta versión de domainatrix son cathparse (genera un archivo DCF a partir de archivos CATH), domainnr (elimina los dominios reduntantes de un archivo DCF), domainreso (elimina dominios de baja resolución de un archivo DCF), domainseqs (añade registros de secuencias a un archivo DCF), domainsse (añadir registros de estructuras secundarias a un archivo DCF), scopparse (genera archivos DCF a partir de archivos SCOP) y ssematch (busca coincidencias de estructuras secundarias en un archivo DCF).

Los programas DOMAINATRIX han sido desarrollados por Jon Ison y sus compañeros en MRC HGMP para su investigación del dominio de las proteínas. Se incluyen como un paquete EMBASSY como un trabajo en curso.

Las aplicaciones que se incluyen en esta versión de domalign son allversusall (similitud de secuencias de datos de la comparación todos-contra-todos), domainalign (genera alineamientos (archivo DAF) para nodos en un fichero DCF), domainrep (re-ordena el fichero DCF para identificar estructuras representativas) y seqalign (extiende alineamientos (fichero DAF) con secuencias (fichero FHD)).

The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Applications in this DOMSEARCH release are seqfraggle (removes fragment sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch (generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove ambiguous classified sequences from DHF files) and seqwords (Generates DHF files from keyword search of UniProt).

EMBOSS («European Molecular Biology Open Software Suite») es un paquete de programas de análisis de código abierto especialmente desarrollado para cubrir las necesidades de la comunidad de usuarios de biología molecular (p.ej. EMBnet). Los programas usan datos en varios formatos automáticamente e, incluso, permiten obtener de forma transparente secuencias de datos de la web. Además, al proporcionarse grandes bibliotecas con el paquete, es una plataforma que permite a otros científicos desarrollar y publicar programas con un verdadero espíritu de código abierto. EMBOSS también integra varios paquetes y herramientas disponibles actualmente para el análisis de secuencias en un entorno integrado. EMBOSS rompe con la tendencia histórica de paquetes de programas comerciales.

Exonerate le permite alinear las secuencias usando muchos modelos de alineamiento, ya sea utilizando programación dinámica exhaustiva, o con una gran variedad de heurística. Gran parte de las funcionalidades de la suite de programación dinámica Wise se re-implementaron en C para una mayor eficiencia. Exonerate es un componente intrínseco de la construcción de las bases de datos del genoma de Ensembl, proporcionando coeficientes de similitud entre las secuencias del ANR y el ADN, permitiendo así determinar las uniones variables y las secuencias de la codificación en general.

Hay un sistema de simulación de experimentos «In-silico PCR» (consulte la página man ipcress) empaquetado con exonerate.

Este paquete también incluye una selección de utilidades para realizar manipulaciones sencillas y de forma rápida con archivos FASTA de más de 2Gb.

fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program.

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

Note that the homepage of this program is not available any more and so this program will probably not see any further updates.

Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes. There was a standard software package for genetic linkage called LINKAGE. FASTLINK is a significantly modified and improved version of the main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation. FASTLINK has been used in over 1000 published genetic linkage studies.

This package contains the following programs:

 ilink:    GEMINI optimization procedure to find a locally
           optimal value of the theta vector of recombination
           fractions
 linkmap:  calculates location scores of one locus against a
           fixed map of other loci
 lodscore: compares likelihoods at locally optimal theta
 mlink:    calculates lod scores and risk with two of more loci
 unknown:  identify possible genotypes for unknowns

El objetivo de FastQC es proporcionar una forma sencilla de realizar algunas comprobaciones de control de calidad de los datos de secuencia sin procesar procedentes de canales de secuenciación de alto rendimiento. Proporciona un conjunto modular de análisis que puede utilizar para obtener una impresión rápida sobre si sus datos tienen algún problema del que debería ser consciente antes de realizar cualquier análisis posterior.

Las principales funciones de FastQC son

• Importar datos desde archivos BAM, SAM o FastQ (cualquier variante)

• Proporcionar una visión general rápida para informarle en qué áreas puede haber problemas

• Gráficos y tablas de resumen para evaluar rápidamente sus datos

• Exportar los resultados a un informe permanente basado en HTML
• Operar fuera de línea para permitir la generación automática de informes sin necesidad de ejecutar la aplicación interactiva.

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It handles alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

FastTree is more accurate than PhyML 3 with default settings, and much more accurate than the distance-matrix methods that are traditionally used for large alignments. FastTree uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992) model of amino acid evolution. To account for the varying rates of evolution across sites, FastTree uses a single rate for each site (the "CAT" approximation). To quickly estimate the reliability of each split in the tree, FastTree computes local support values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local supports").

This package contains a single threaded version (fasttree) and a parallel version which uses OpenMP (fasttreMP).

Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses.

fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm.

Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.

Parameter names changed in Flexbar. Please review scripts. The recent months, default settings were optimised, several bugs were fixed and various improvements were made, e.g. revamped command-line interface, new trimming modes as well as lower time and memory requirements.

FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the command line tool freecontact(1).

One goal of sequencing based metagenomic analysis is the quantitative taxonomic assessment of microbial community compositions. However, the majority of approaches either quantify at low resolution (e.g. at phylum level) or have severe problems discerning highly similar species. Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods.

The GenomeTools contains a collection of useful tools for biological sequence analysis and -presentation combined into a single binary.

The toolkit contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization, and much more.

A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot:

• Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets.
• All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file.
• Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement.
• All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients.
• Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes.
• The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error.
• gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape.
• You can draw different alignments on same alignment plot and distinguish them by using different colors for each.
• Shape dictionary has been expanded, so that further feature shapes are now available (see manual).
• Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows one to show color pseudo-blending when horizontal and vertical ribbons overlap.

gff2ps es un script desarrollado con el ánimo de convertir registros con formato gff a gráficos unidimensionales de alta calidad en PostScript. Estos gráficos pueden ser útiles para comparar estructuras genómicas y para ver la salida de programas de notación genómica. Se puede usar de una manera muy sencilla, porque asume que el archivo gff lleva por sí mismo suficiente información de formato, pero también permite un gran grado de personalización a través de opciones y/o un archivo de configuración.

GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. It was foremost designed for prokaryotic gene prediction and is able to resolve genes within the expressed region of an operon. However, it is also applicable to eukaryotes and predicts exon intron structures as well as alternative isoforms.

GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.

This package includes programs for discovering motifs shared by a set of sequences and finding matches to these motifs in a sequence database, as well as utilities for converting glam2 motifs to standard alignment formats, masking glam2 motifs out of sequences so that weaker motifs can be found, and removing highly similar members of a set of sequences.

The package includes these programs:

 glam2:       discovering motifs shared by a set of sequences;
 glam2scan:   finding matches, in a sequence database, to a motif discovered
              by glam2;
 glam2format: converting glam2 motifs to  standard alignment formats;
 glam2mask:   masking glam2 motifs out of sequences, so that weaker motifs
              can be found;
 glam2-purge: removing highly similar members of a set of sequences.

In this binary package, the fast Fourier algorithm (FFT) was enabled for the glam2 program.

This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of

• known splice sites and identify novel splice sites.
• known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.

Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains variants both for execution on a single machine, and using the MPI interface across multiple machines.

HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

This package contains HHsearch and HHblits among other programs and utilities.

HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling.

HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments.

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

HMMER es una implementación de los métodos del modelo de Markov de perfiles ocultos para búsquedas en bases de datos de secuencias biológicas usando alineamientos múltiples como consultas.

Dado un alineamiento múltiple de secuencias como entrada, HMMER construye un modelo estadístico llamado modelo oculto de Markov que se puede usar como una consulta a una base de datos de secuencias para encontrar (y/o alinear) homólogos adicionales de la familia de secuencias.