http://bioinf.comav.upv.es/sff_extract/index.html, This program will convert paired-end sff files into paired-end fastq files.

duncanca / mosaik-aligner. Another warning about this program, the input file must be in the current directory, HMMER updated from version 3.1b1 to version 3.1b2, LinkImpute version 1.1 and LinkImputeR version 1.1.1, ABySS-Explorer - Novel graph-based representation of sequence assembly, AliView - Lightweight alignment viewer and editor, Bambino - A graphical viewer and variant detector for NGS files in SAM/BAM format, BAMseek - A Large File Viewer for BAM and SAM alignment files, Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily, BAPS - Bayesian Analysis of Population Structure, FigTree - Graphical viewer of phylogenetic trees, Geneland - Statistical analysis of population genetics data, Genomica - Analysis and visualization tool for genomic data, Mesquite - A modular system for evolutionary analysis, MochiView - Integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis, SeqGrapheR - Repeat Cluster Visualization, Structure - Investigate population structure with multi-locus genotype data, Structure Harvester - A website and program for visualizing STRUCTURE output, SyMAP - Synteny Mapping and Analysis Program, Tablet - Next Generation Sequence Assembly Visualization, TASSEL - Trait Analysis by aSSociation, Evolution, and Linkage, TreeGraph - Generating complex PostScript and SVG trees using an extensible tree description format, TreeGraph 2 - A graphical editor for phylogenetic trees, TreeLD - Tool for mapping complex trait loci, UGENE - Free open-source cross-platform bioinformatics software, Annovar - Functionally annotate genetic variants. They are designed for the Illumina sequencing platform and they can return all possible map locations for improved structural variation discovery. Copy of manual included with primer3, The current 2.3.6 version programs are available in the default PATH, however the older This program was written by Indraniel Das, web site http://indraniel.wordpress.com/2010/04/23/sff2fastq/ inSilicoDigestor_multi_1.32.py to run it, e.g. Performs a full Smith Waterman alignment. Some default parameters from clustalx for reference: http://bozeman.mbt.washington.edu/consed/consed.html, consed is in the default PATH for all users. Mac computers (it has not been tested on Windows operating systems).

Ungapped alignment that takes into account quality scores for each base. In conclusion, we show that different aligner tools have varying performances in regard to accuracy, speed, and memory usage. Dindel - Dindel: Accurate indel calls from short-read data, DISTRUCT - A program for the graphical display of population structure, EDirect - Entrez Direct: E-utilities on the UNIX Command Line, EMBOSS - A package of free, Open Source software for molecular biology, EST_GENOME - A program to align a spliced DNA sequence to an unspliced genomic sequence, GapFiller - Closing gaps within pre-assembled scaffolds, Geometric Analysis of Structural Variants, The Genome Analysis Toolkit or The GATK - Analyse next-generation resequencing data, Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects, http://plntfdb.bio.uni-potsdam.de/v3.0/fam_mem.php?family_id=CCAAT, http://bioinfo.cau.edu.cn/ProFITS/kinase.php, http://pfam.sanger.ac.uk/family/PF00069.18, http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf, https://github.com/lindenb/jvarkit/wiki/_pages, mesquite - A modular system for evolutionary analysi, http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf, MOSAIK is a reference-guided aligner for next-generation sequencing technologies, Whole genome sequencing and variant discovery in C. elegans.pdf, Micro-read substitution-only Fast Alignment Search Tool, MUMmer - Ultra-fast alignment of large-scale DNA and protein sequences, MView - Reformats a sequence database search or a multiple alignment, Newick Utilities - Shell tools for processing phylogenetic trees, Teune & Steger (2010) J. Nucleic Acids 2010, European Bioinformatics Institute (EMBL-EBI), http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889/, Picard - Java-based command-line utilities that manipulate SAM files, Pilon - Automatically improve draft assemblies, find variation among strains, including large event detection, PipMaker and MultiPipMaker - Compute alignments of similar regions in two DNA sequences, PlantTFcat - Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis, Platypus - A Haplotype-Based Variant Caller For Next Generation Sequence Data, PRINSEQ - PRe-process and show INformation of SEQuence data, http://www.genomesavant.com/p/savant/learn, http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/Help/, http://www.bioinformatics.babraham.ac.uk/training.html#seqmonk, seqtk - Toolkit for processing sequences in FASTA/Q formats, http://www.ncbi.nlm.nih.gov/Sequin/download/seq_unix_download.html, http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html, http://indraniel.wordpress.com/2010/04/23/sff2fastq/, http://www.ncbi.nlm.nih.gov/spidey/spideydoc.html, Splicegrapher - Splice graphs of alternate splicing patterns, SplitsTree4 - Compute unrooted phylogenetic networks from molecular sequence data, sprai - single pass read accuracy improver, sra Toolkit - Short Read Archive Toolkit from NCBI, http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software, SSAHA2 - Sequence Search and Alignment by Hashing Algorithm, http://pritch.bsd.uchicago.edu/structure_software/release_versions/, http://taylor0.biology.ucla.edu/structureHarvester/, undocumented change to TASSEL4 standalone, http://pritch.bsd.uchicago.edu/treeld/TreeLD_Doc/Documentation.html, svtyper - Bayesian genotyper for structural variants, TIGRA - Targeted local assembly of structural variant breakpoints, TopHat - A fast splice junction mapper for RNA-Seq reads, TopoView - Track for RNAseq data in GBrowse, TransDecoder - Find Coding Regions Within Transcripts, treemix - Inference of population trees with admixture, Trimmomatic - A flexible read trimming tool for Illumina NGS data, Trinotate - Transcriptome Functional Annotation and Analysis, tRNAscan-SE - Search for tRNA genes in genomic sequence, http://lowelab.ucsc.edu/tRNAscan-SE/Manual/Manual.html, USEARCH - A unique high-throughput sequence analysis tool, VCF2Dis - p-distance matrix based Variant Call Format, VCFtools - Methods for working with VCF files, http://dx.doi.org/10.1093/bioinformatics/btr330, Velvet - Sequence assembler for very short reads, vg - Tools for working with variation graphs, VSEARCH - Open source alternative to USEARCH, wgsim - Sequence assembler for very short reads, wQMC - Phylogenic tree using the Weighted Quartet MaxCut Algorithm, example_input_file_for_wQMC_20_leaves.txt, XPCLR - Allele frequency differentiation at linked loci to detect selective sweeps.

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