Debian Med Cloud packages

ABySS는 짧은 읽기를 위해 설계된 de novo, 병렬, 시퀀스 어셈블러입니다. 게놈 또는 전사체 시퀀스 데이타를 조립하는데 사용될 수 있습니다. 병렬화는 MPI, OpenMP, pthread를 사용해서 수행됩니다.

This package collects all those smallish applications that acedb collects under its 'other' target of its Makefile.

efetch: presumably short for 'entry fetch' collects sequence information from common DNA and protein databases.

Aevol은 디지탈 유전학 모델입니다: 디지탈 유기체의 개체군은 선택과 변이 과정을 거쳐 다윈의 역학을 만들어 냅니다.

선택 특성 (예, 모집단 크기, 환경 유형, 환경 변화) 또는 변동 (예, 돌연변이율, 염색체 재배열율, 재배열 유형, 수평 이동)을 수정함으로써 이러한 매개 변수가 진화된 유기체의 구조에 미치는 영향을 실험적으로 연구할 수 있습니다. 특히 Aevol은 정확하고 현실적인 게놈 모델을 통합하기 때문에 게놈의 구조적 변이 (예, 유전자 수, synteny, 코딩 서열 비율)를 연구 할 수 있습니다.

시뮬레이션 플랫폼은 계통 발생을 분석하고 진화에 따른 유기체 및 개체군의 여러 특성을 측정하기 위한 도구 세트와 함께 제공됩니다.

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into Artemis genome viewer freely available at: 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.

AmpliconNoise는 높은 처리량의 시퀀스 데이타를 정리하는 어플리케이션 패키지 입니다. 3개의 메인 파트로 구성됩니다:

Pyronoise - 잘못 해석된 곳을 플로우그램 기반 클러스트링 처리 SeqNoise - PCR 포인트 변이 제거 Perseus - 레퍼런스 시퀀스 집합에 대한 필요가 없이 PCR 키메라 제거

이전에는 동일한 개발자가 만든 독립 실행형 "Pyronoise"가 있었고 이 패키지는 업데이트된 버젼을 포함합니다. Qiime에는 관련있는 "Denoiser"가 있지만 서로 별개입니다.

Anfo는 Soap/Maq/Bowtie 정신을 따르는 매퍼지만, 구현에는 BLAST/BLAT 이후 더 많은 시간이 걸립니다. 이는 DNS 시퀀스가 어떻게든 수정되거나 (고대 DNA 또는 중아황산염 처리를 생각) 빠른 매퍼가 정상적으로 처리하는 것보다 샘플과 참조 사이에 더 많은 차이가 있는 시퀀싱 읽기 정렬에 가장 유용합니다 (예: 참조 게놈이 누락되는 대신 관련 종이 사용됩니다)

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 is a prime representative of the programs addressing the simulation of the docking of fairly small chemical ligands to rather big protein receptors. Earlier versions had all flexibility in the ligands while the protein was kept rather ridgid. This latest version 4 also allows for a flexibility of selected sidechains of surface residues, i.e., takes the rotamers into account.

The AutoDock program performs the docking of the ligand to a set of grids describing the target protein. AutoGrid pre-calculates these grids.

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

AutoDockSuite는 알려진 3차원 구조의 수용체에 대해서 더 작은 화합물의 도킹에 대한 분자 분석을 다룹니다.

AutoGrid 프로그램은 단백질이 점 전하에 미치는 영향을 설명하는 그리드 세트에 리간드를 도킹하기 위한 사전 계산을 수행합니다. 리간드에 대한 이러한 힘의 효과는 AutoDock 프로그램에 의해 분석됩니다.

BamTools은 BAM 파일을 사용해서 연국 분석 및 데이타 관리를 용이하게 합니다. 현재 시퀀싱 기술로 생성된 엄청난 양의 데이타를 처리합니다. 이 데이타는 생물 정보학 연구에서 일반적으로 사용되는 텍스트 기반 파서에 의해 쉽게 처리되지 않는 바이너리 형식, 일반적으로 압축된 상태로 저장됩니다.

BamTools는 BAM 파일 지원 및 명령행 툴킷 모두를 위한 C++ API를 제공합니다.

이 패키지는 bamtools 명령행 툴킷입니다.

사용 가능한 bamtools 명령:

 convert  BAM과 다른 여러 형식간 변환
 count    BAM 파일에서 정렬을 인쇄
 coverage 입력된 BAM 파일에서 범위 통계를 인쇄
 filter   사용자 지정 기준에 따라 BAM 파일 필터링
 header   BAM 헤더 정보 인쇄
 index    BAM 파일용 인덱스 생성
 merge    여러 BAM 파일을 하나의 파일로 병합
 random   기존의 BAM 파일에서 임의 정렬을 선택, 테스팅 도구로 더 많이
          사용.
 resolve  쌍방향 읽기 해결 (필요에 따라 IsProperPair 플래그 표시)
 revert   중복 마크 제거 및 원래 기본 품질 복구
 sort     몇몇 기준에 따라 BAM 파일 정렬
 split    사용자 지정 속성에서 BAM 파일 분할, 발견된 각 값에 대한
          새로운 BAM 출력 파일 생성
 stats    입력 BAM 파일에서 몇가지 기본 통계 인쇄

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.

The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl.

The recommended packages are needed to run some of the included binaries, for a detailed explanation including the specific Perl modules please see README.Debian.

The suggested package enhances the manual pages.

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 is a library of C code functions for sequence analysis. It also includes a number of small utility programs to convert, show statistics, manipulate and do other functions on sequence files.

The original name of the package is "squid", but since there is already a squid on the archive (a proxy cache), it was renamed to "biosquid".

This package contains some tools to demonstrate the features of the SQUID library.

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

이 패키지는 최신 (2010) DNA 염기서열 분석 기술의 결과를 해석하기 위해 문제를 해결합니다. 이는 상당히 짧은 범위를 생성하며 작접적으로 해석할 수 없습니다. Bowtie와 같은 도구는 실행당 시퀀싱된 DNA의 짧은 길이에 염색체 위치를 제공하는 것은 어려운 일입니다.

Bowtie는 짧은 DNA 서열 (읽기)을 시간당 2,500만 개 이상의 35bp 시간당 읽기 속도로 인간 게놈에 정렬합니다. Bowtie는 메모리 공간을 작게 유지하기 위해 Burrows-Wheeler 인덱스로 게놈을 인덱스화합니다: 일반적으로 인간 게놈의 경우 2.2GB (페어드 엔드의 경우 2.9GB) 입니다.

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 is a program for creating good looking printouts from multiple-aligned protein or DNA sequences. The program does not perform the alignment by itself and requires as input a file that was created by a multiple alignment program or manually edited with respective tools.

Boxshade reads multiple-aligned sequences from either PILEUP-MSF, CLUSTAL-ALN, MALIGNED-data and ESEE-save files (limited to a maximum of 150 sequences with up to 10000 elements each). Various kinds of shading can be applied to identical/similar residues. Output is written to screen or to a file in the following formats: ANSI/VT100, PS/EPS, RTF, HPGL, ReGIS, LJ250-printer, ASCII, xFIG, PICT, 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.

Circos는 원형 배치로 데이타를 시각화합니다 - 원형배치는 객체 또는 위치간 관 계 탐색 및 매우 유용한 출판 품질 그래픽을 만드는데 이상적입니다.

이 패키지는 (gnuplot와 같이) 명령행으로 구동되고 스크립트를 완벽하게 지원하 는 Circos 플로터 엔진을 제공합니다.

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.

ClonalFrame은 클론 상속을 중단한 상동 재조합 이벤트 염색체 위치를 추정하면 서, 샘플 멤버들 사이에 클론 관계를 식별합니다.

전체 게놈에서 단일 조각 DNA를 통해, Clonalframe을 임의의 시퀀스 데이타에도 적용할 수 있습니다. 이는 7 유전자 단편이 시퀀스된, MLST 데이타 분석에 꽤 적 합하지만, 시퀀스된 영역이 전체 게놈에 길이와 수를 증가함으로 점차 더 강력해 집니다. 하지만 이는 정렬된 시퀀스를 요구합니다. 정렬되지 않은 게놈 데이타를 가지고 있을 경우, ClonalFrame 분석에 필요한 정확한 형식으로 전체 박테리아 게놈을 정렬하는 Mauve 사용을 권장합니다.

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 Datamash는 입력 텍스트 데이타 파일에서 기본 숫자, 텍스트 및 통계 연산을 수행하는 명령행 프로그램입니다. 이식 가능하고 신뢰있게 설계되었으며, 연구원이 코드 또는 짧은 스크립트를 만들지 않고도 분석 파이프라인을 쉽게 자동화 할 수 있도록 합니다.

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 is a command line tool to perform multiple alignment of protein or DNA sequences. It is a complete reimplementation of the segment-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2.2 and DIALIGN-T. For pairwise alignment, DIALIGN-TX uses a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, DIALIGN-TX uses an improved greedy procedure that is less sensitive to spurious local sequence similarities.

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'는 시스테인의 이황화 결합 상태와 염기 서열만으로 시작하는 이들의 이황화 연결성을 예측하기위한 것입니다. 이황화 가교는 여러 단백질의 폴딩 과정을 안정화하는 데 중요한 역할을합니다. 따라서 서열만으로 이황화 가교를 예측하는 것은 특정 단백질의 구조 및 기능적 특성을 연구하는 데 유용합니다. 또한 시스테인의 이황화 결합 상태에 대한 지식은 실험 구조 결정 과정에 도움이 될 수 있으며 다른 게놈 주석 작업에 유용 할 수 있습니다.

'disulfinder'는 두 가지 계산 단계에서 이황화 패턴을 예측합니다: (1) 각 시스테인의 이황화 결합 상태는 BRNN-SVM 이원 분류기에 의해 예측됩니다. (2) 브리지 형성에 참여하는 것으로 알려진 시스테인은 연결 패턴을 얻기 위해 재귀 신경망에 의해 쌍을 이룹니다.

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.

The DOMAINATRIX 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 the current domainatrix release are cathparse (generates DCF file from raw CATH files), domainnr (removes redundant domains from a DCF file), domainreso (removes low resolution domains from a DCF file), domainseqs (adds sequence records to a DCF file), domainsse (adds secondary structure records to a DCF file), scopparse (generates DCF file from raw SCOP files) and ssematch (searches a DCF file for secondary structure matches).

The DOMALIGN 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 the current domalign release are allversusall (sequence similarity data from all-versus-all comparison), domainalign (generates alignments (DAF file) for nodes in a DCF file), domainrep (reorders DCF file to identify representative structures) and seqalign (extend alignments (DAF file) with sequences (DHF file)).

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 is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general.

An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate.

This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 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.

유전자 연관 분석은 유전자 지도 및 유전자 질병의 대략적인 위치를 찾는데 사용 되는 통계적 기법입니다. LINKAGE라 불리는 유전적 연관을 위한 표준 소프트웨어 패키지가 있습니다. FASTLINK는 더 빠르게 순차적으로 실행되고, 병렬로 실행할 수 있으며, 컴퓨터 문제에서 사용자가 정상적으로 복구 할 수 있도록 하며, 그리 고 풍부한 새로운 문서를 제공하는 LINKAGE 메인 프로그램의 크게 개선된 버젼입 니다. FASTLINK는 1000개 이상의 발표된 유전적 연관 연구를 통해 사용되어 왔습 니다.

이 패키지는 다음과 같은 프로그램이 포함되어 있습니다:

 iLink: 조환비율 벡터의 내부적 세타 최적값을 찾기 위한 GEMINI 최적화 절차
 linkmap: 다른 유전자자리들의 고정된 지도에 대한 하나의 유전자자리의 위치
          점수 계산
 lodscore: 내부 최적 세타에서 가능성 비교
 MLINK: LOD 점수와 두개의 더 많은 유전자자리 위험 계산
 unknown: 알려지지 않은 것을 위해 가능한 유전형을 확인

FastQC는 처리량이 높은 시퀀스 파이프라인에서 발생하는, 원시 시퀀스 데이타에 대한 몇가지 품질 관리 검사를 간단하게 수행할 수 있는 방법을 제공합니다. 추가 분석을 수행하기 전에 데이타에 알아야 할 문제가 있는지 여부를 신속하게 파악할 수 있는 모듈식 분석 집합을 제공합니다.

FastQC의 주요기능은 아래와 같습니다.

• BAM, SAM 또는 FastQ 파일에서 데이타 가져오기 (모든 변형)
• 문제가 발생할 수 있는 영역을 당신에게 알려줄 빠른 개요 제공
• 데이타를 빠르게 평가 할 수 있는 요약 그래프 및 테이블
• 결과를 HTML 기반 영구 보고서로 내보내기
• 대화형 어플리케이션을 실행하지 않고도 보고서를 자동으로 생성할 수 있는 오프라인 작업

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 is a script program developed with the aim of converting gff-formatted records into high quality one-dimensional plots in PostScript. Such plots maybe useful for comparing genomic structures and to visualizing outputs from genome annotation programs. It can be used in a very simple way, because it assumes that the GFF file itself carries enough formatting information, but it also allows through a number of options and/or a configuration file, for a great degree of customization.

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 is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries.

Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family.