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454 gsAssembler or gsMapper2.8LinuxAssembly and alignment software for 454 or other long reads.12/13/20113/24/2014detailed information
a520150522LinuxA genome assembly pipeline for bacteria and archaea10/14/20136/3/2016detailed information
ABruijn20161221LinuxABruijn is a de novo assembler for PacBio and Oxford Nanopore Technologies reads. 12/21/2016 detailed information
ABySS 1.9.0LinuxIllumina short reads assembly tool.12/13/20115/9/2016detailed information
AdapterRemoval2.1.1LinuxRemove adapters from sequences in either single end or paired end experiments9/16/2015 detailed information
Admixtools1.1LinuxThe ADMIXTOOLS package implements 5 methods described in Patterson et al (2012) Ancient Admixture in Human History.11/6/20131/22/2015detailed information
Admixture1.23LinuxSoftware tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.2/19/20142/19/2014detailed information
Alder1.03LinuxThe ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture.11/6/201311/6/2013detailed information
AlleleSeq1.1LinuxDetects SNVs from ChIP-seq or RNA-seq experiments.4/2/2014 detailed information
ALLMAPS20150710LinuxALLMAPS is capable of computing a scaffold ordering that maximizes the colinearity to a collection of maps, including genetic, physical or comparative maps into the final chromosome build.7/10/2015 detailed information
ALLPATHS-LG49148LinuxIllumina short reads assembly tool.12/14/201112/5/2014detailed information
AMOS3.1.0LinuxAMOS is a collection of tools and class interfaces for the assembly of DNA reads. 1/12/20131/14/2013detailed information
analysis0.8.4Linux C++ software for evolutionary genetic analysis.9/2/2014 detailed information
ANGSD0.911LinuxANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities.3/27/20154/14/2016detailed information
Annovar20130823LinuxSNP/INDEL annotation.12/13/20111/22/2015detailed information
Atlas-Link2050709LinuxAtlas-Link links and orients genome sequence contigs quickly and accurately using mate-pair information.7/9/2015 detailed information
ATLAS_GapFill2.2LinuxATLAS GapFill deals with the repetitive gap assembly problem by using the unique gap-flanking sequences to group reads and convert the problem to a local assembly task.7/9/2015 detailed information
ATSAS 2.5.0-2LinuxA program suite for small-angle scattering data analysis from biological macromolecules.12/13/20111/31/2013detailed information
Augustus3.2.1LinuxAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences1/23/20131/22/2016detailed information
bamtools2.3.0LinuxBAM file processing and filtering.12/13/20113/24/2014detailed information
BayeScan2.1LinuxBayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.11/24/2014 detailed information
BBmap35.66LinuxThis package includes BBMap, a short read aligner, as well as various other bioinformatic tools.11/6/2015 detailed information
BCFtools1.3.1Linuxbcftools — utilities for variant calling and manipulating VCFs and BCFs.2/20/2017 detailed information
Beagle3.3.2LinuxPhasing, imputation, Haplotype inferrance11/18/20133/24/2014detailed information
Beagle44.1LinuxBeagle4 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. It does not perform association testing.8/22/201410/24/2016detailed information
Beast220170327LinuxBEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.3/27/2017 detailed information
bedops2.4.15LinuxFast BED file operaion.7/26/20133/25/2016detailed information
BEDtools2.26.0LinuxBED file operation.2/6/20121/25/2017detailed information
bfc20150417LinuxHigh-performance error correction for Illumina resequencing data10/18/2016 detailed information
bgc1.01Linuxbgc implements Bayesian estimation of genomic clines to quantify introgression at many loci.2/12/20132/12/2013detailed information
biobambam0.0.125LinuxThis package contains tools for processing BAM files.2/28/20142/28/2014detailed information
Bioconductor3.0LinuxR package for genomics data analysis.7/19/20133/24/2014detailed information
BioPerl1.6.922LinuxPERL library for general bioinformatics.12/13/20113/24/2014detailed information
BioPython1.60Linux 2/27/20121/31/2013detailed information
Birdsuite1.5.5LinuxSet of tools to detect and report SNP genotypes, common CNPs, and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform.4/11/2014 detailed information
Bismark0.16.1LinuxA bisulfite read mapper and methylation caller 11/20/20126/30/2016detailed information
blasr20170117LinuxThe PacBio long read aligner9/24/20142/3/2017detailed information
BLAST2.3.0LinuxSequence alignment.12/13/20112/9/2016detailed information
blast2goDB: Mar.2016; Software: v1.2.1LinuxGene Ontology annotation and function enrichment analysis.4/15/20134/25/2016detailed information
BLAT34LinuxSequence alignment.12/13/20115/1/2012detailed information
bmtagger2/21/14LinuxBest Match Tagger for removing human reads from metagenomics datasets10/6/2016 detailed information
Boost1.57.0LinuxBoost provides free peer-reviewed portable C++ source libraries.12/17/2014 detailed information
Bowtie1.1.2LinuxAn ultrafast, memory-efficient short read aligner.12/13/20113/22/2016detailed information
Bowtie22.3.0LinuxAn ultrafast, memory-efficient short read aligner.5/1/20121/25/2017detailed information
breseq0.27.2Linuxbreseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes. breseq is a command line tool implemented in C++ and R. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads (such as those produced by new mobile element insertions) in an annotated HTML format.6/29/2016 detailed information
BSseeker22.1.0LinuxMapping the bisulfite-treated short reads1/23/2017 detailed information
BUSCO2.0LinuxAssessing genome assembly and annotation completeness.1/22/20163/20/2017detailed information
BWA0.7.13LinuxBWA is a software package for mapping low-divergent sequences against a large reference genome.12/13/20113/22/2016detailed information
canu1.3Linuxassemble pacbio reads2/11/201611/4/2016detailed information
CAP312/21/07LinuxA DNA Sequence Assembly Program4/4/2014 detailed information
CBSU RNAseq1.0Linux 12/13/20115/1/2012detailed information
cd-hit4.6.1Linuxcluster reads based on sequence similarity9/28/2015 detailed information
CEGMA2.5LinuxCEGMA (Core Eukaryotic Genes Mapping Approach) is a tool for building a highly reliable set of gene annotations in the absence of experimental data.1/16/2015 detailed information
CheckM1.0.7LinuxCheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes10/11/2016 detailed information
Circos0.67-7LinuxCircos is a software package for visualizing data and information.3/24/2015 detailed information
Circuitscape4.0.5LinuxAn open-source program that uses circuit theory to model connectivity in heterogeneous landscapes4/16/2015 detailed information
CLUMPP1.1.2LinuxCLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses.4/10/2017 detailed information
Clustal Omega LinuxMultiple sequence alignment2/24/2015 detailed information
CLUSTALW2.1LinuxGeneral purpose DNA or protein multiple sequence alignment program for three or more sequences.12/13/20115/1/2012detailed information
Cluster1.52LinuxThe open source clustering software implementing the most commonly used clustering methods for gene expression data analysis.4/28/2014 detailed information
CNVnator0.3LinuxA tool for CNV discovery and genotyping from depth of read mapping6/23/20156/23/2015detailed information
CrossMap0.2.5LinuxCrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies.5/11/201610/13/2016detailed information
CRT LinuxCRISPR Recognition Tool3/24/2017 detailed information
Cufflinks2.2.1LinuxRNA-seq reference guided transcript assembly, quantification and differential expressed gene identification12/13/20115/6/2014detailed information
cutadapt1.8.1Linuxcutadapt removes adapter sequences from high-throughput sequencing data.10/11/20134/2/2014detailed information
dadi1.7.0LinuxIt implements a method for demographic inference from genetic data, based on a diffusion approximation to the allele frequency spectrum.5/12/2015 detailed information
DeconSeq0.4.3LinuxDECONtamination of SEQuence data using a modified version of BWA-SW11/6/2015 detailed information
deepTools2.3.5LinuxA suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data.10/14/2016 detailed information
delly0.6.5LinuxDELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. 11/13/20135/4/2015detailed information
destruct1.1Linuxdistruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs.4/10/2017 detailed information
DETONATE1.10LinuxBoth packages are mainly intended to be used to evaluate de novo transcriptome assemblies2/16/2016 detailed information
diamond0.8.4LinuxDIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.11/24/20141/25/2017detailed information
Discovar52488LinuxDISCOVAR is a small genome assembler and variant caller from Broad Institute. Uses 250pb PE PCR-free Illumina reads.8/11/20142/12/2016detailed information
Discovar de novo52488LinuxExperimental de novo assembler for large genomes using 250pb PE PCR-free Illumina reads. From Broad Institute.8/11/20142/12/2016detailed information
distruct1.1Linuxdistruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs. 4/10/2017 detailed information
Docker1.12.5LinuxExecutes applications in containers that are isolated from main operating system (OS-level virtualization)2/14/2017 detailed information
dREG20161118LinuxDetection of Regulatory DNA Sequences using GRO-seq Data.4/28/201611/18/2016detailed information
dsk1.6706LinuxDSK is a k-mer counting software, similar to Jellyfish.10/17/2014 detailed information
ea-utilsrev822LinuxCommand-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc.3/10/2015 detailed information
ecopcr0.5.0LinuxDNA barcoding is a tool for characterizing the species origin using a short sequence9/3/2015 detailed information
EDGE1.1LinuxNext Generation Sequencing pipeline6/8/2016 detailed information
EIGENSOFT5.0.1LinuxThe EIGENSOFT package combines functionality from population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction method (Price et al. 2006).10/14/201310/14/2013detailed information
EMBOSS6.6.0LinuxEuropean Molecular Biology Open Software Suite11/6/201311/6/2013detailed information
ermineJ3.0.2LinuxErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing something interesting" in an experiment that generates long lists of candidates. 9/22/2016 detailed information
exabayes1.4.1LinuxExaBayes is a software package for Bayesian tree inference. 2/16/20162/16/2016detailed information
exonerate2.2.0Linuxexonerate is a generic tool for pairwise sequence comparison1/23/20131/23/2013detailed information
eXpress1.5.1LinuxA streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences9/25/2014 detailed information
FALCON20160919LinuxFalcon Genome Assembly Tool Kit (PacBio)4/28/20169/19/2016detailed information
FALCON_unzip20160919LinuxFor Phased Diploid Genome Assembly with PacBio reads.9/19/2016 detailed information
Fast-GBS20170110Linux Extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries.1/23/2017 detailed information
fasta36.3.8dLinuxSequence search and alignment including global alignment.2/7/2017 detailed information
FastML20150324LinuxMaximum Likelihood ancestral sequence reconstruction3/24/2015 detailed information
fastq_species_detector1LinuxBLAST a sample of eads form a fastq file agains nt database and determine fractions of reads with best matches to different speices7/17/2014 detailed information
FastQC0.11.5LinuxA quality control tool for high throughput sequence data.4/16/20133/22/2016detailed information
fastStructure1.0LinuxfastStructure is a fast algorithm for inferring population structure from large SNP genotype data2/15/2017 detailed information
FastTree2.1.7LinuxFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.3/24/2015 detailed information
FASTX0.0.13LinuxA collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.12/13/201110/1/2013detailed information
fineSTRUCTURE2.0.6LinuxPipeline for running ChromoPainter and FineSTRUCTURE for population inference9/14/2015 detailed information
flash1.2.10LinuxFLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments.11/21/20131/22/2015detailed information
Flexible Adapter Remover2.15LinuxFAR (The Flexible Adapter Remover) is a program that removes adapter sequences from deep sequencing data in FASTA/Q, CSFASTA/Q format (Illumina / Roche 454 / SOLiD Colorspace). It also demultiplexes barcoded runs.8/1/20128/1/2012detailed information
FMAP20170125LinuxFunctional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.11/15/20161/25/2017detailed information
freebayesv1.0.2LinuxBayesian haplotype-based polymorphism discovery and genotyping.5/21/20144/14/2016detailed information
GATK3.7LinuxThe Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data.12/13/20114/8/2017detailed information
GCTA1.25.2LinuxGCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.2/17/20143/26/2016detailed information
GEM library20121106-022124LinuxLibrary of efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT).10/4/2016 detailed information
GEMMA0.94LinuxGenome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS). 4/16/2014 detailed information
geneid1.4.4Linuxgeneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.1/16/2015 detailed information
GeneMark4.30LinuxThis program combines GeneMark.hmm (prokaryotic) and GeneMark (prokaryotic) with a self-training procedure that determines parameters of the models of both GeneMark.hmm and GeneMark.12/6/20133/26/2016detailed information
GeneMarkerlatestWindowsGenotype analysis software 9/11/2014 detailed information
Genome STRiP1.03.619LinuxGenome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals, but can also process single genomes.7/27/20121/31/2013detailed information
GenomeMapper0.4.4LinuxGenomeMapper is a short read mapping tool designed for accurate read alignments.4/3/2016 detailed information
GenomeStudio (Illumina)2011.1WindowsVisualize and analyze data generated on Illumina's genotyping array platforms with GenomeStudio Data Analysis Software12/13/20119/11/2014detailed information
GenomicConsensus20170217LinuxApply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.2/17/2017 detailed information
germline1.5.1LinuxGERMLINE is an algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing. 1/23/2015 detailed information
GMAP/GSNAP2017-03-17LinuxGMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program5/19/20144/5/2017detailed information
GNU Compilers5.3.0LinuxGNU Compilers package3/2/2016 detailed information
GNU parallel20150422LinuxScript for naive parallelization of a list of tasks 5/20/2015 detailed information
Grinder0.5.4LinuxGrinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.3/28/2017 detailed information
GROMACS5.1.2LinuxGROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.6/25/2016 detailed information
Gubbins20150324LinuxGenealogies Unbiased By recomBinations In Nucleotide Sequences3/24/2015 detailed information
HapCompass0.8.1LinuxA fast cycle basis algorithm for accurate haplotype assembly of sequence data.4/27/2016 detailed information
HAPCUTv0.7LinuxHapCUT is a max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual. It can be applied to sequence data generated from next-generation sequencing platforms. HapCUT takes as input the aligned SAM/BAM files for an individual diploid genome and the list of variants (VCF file), and outputs the phased haplotype blocks that can be assembled from the sequence reads. 10/19/20162/26/2017detailed information
HAPCUT22LinuxHapCUT2 is a maximum-li.kelihood-based tool for assembling haplotypes from DNA sequence reads2/26/2017 detailed information
hapflk1.2.1Linuxhapflk is a software implementing the hapFLK [1] and FLK [2] tests for the detection of selection signatures based on multiple population genotyping data.1/2/20148/28/2015detailed information
HaploMerger20120810LinuxHaploMerger is an effective, easy-to-use, automated pipeline; it is designed to untangle homologous/allelic relationships between two haplotypes in a highly-polymorphic diploid assembly and to guide the subsequent creation of reference haploid assemblies.7/9/2015 detailed information
Haplomerger220151124LinuxHaploMerger2 is an effective, easy-to-use, automated pipeline; it is designed to untangle homologous/allelic relationships between two haplotypes in a highly-polymorphic diploid assembly and to create high-quality reference and alternative haploid assemblies.1/19/2016 detailed information
HapSeq2June 5, 2013LinuxHapSeq2 is a program for genotyping calling and haplotype phasing from next generation sequencing data using haplotype information from jumping reads.2/10/20142/10/2014detailed information
HiC-Pro2.7.9LinuxAn optimized and flexible pipeline for Hi-C data processing.11/29/2016 detailed information
HISAT22-2.0.4LinuxHISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads.6/8/2016 detailed information
HMMER3.1b2LinuxHMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).11/15/20138/4/2016detailed information
HOTSPOT4LinuxHotspot is a program for identifying regions of local enrichment of short-read sequence tags mapped to the genome using a binomial distribution model. Regions flagged by the algorithm are called "hotspots".7/26/20137/26/2013detailed information
HTSeq0.6.1LinuxHTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.10/11/20133/18/2014detailed information
HUMAnN220160712LinuxHUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads)7/12/2016 detailed information
HyPhy2.1.2-0-g63e118dLinuxHyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.2/20/20125/2/2012detailed information
iAssembler1.3.2LinuxiAssembler is a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs. 12/13/20111/31/2013detailed information
IBDLD3.31LinuxA C++ program for multipoint IBD estimation based on high density SNP genotype data.6/23/2015 detailed information
IDBA-UD1.1.1LinuxIDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.6/11/2014 detailed information
IGV2.3.12LinuxThe Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.12/13/20111/9/2014detailed information
IMAGE2.4LinuxIMAGE is a software designed to close gaps in any draft assembly using Illumina paired end reads.4/21/2015 detailed information
impute22.3.0LinuxIMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009: PLoS Genetics 5(6): e1000529.12/19/201312/19/2013detailed information
InStruct7_28_2016LinuxBayesian MCMC Global Population Structure Analysis Program7/28/2016 detailed information
InteMAP1.0LinuxIntegrates three assemblers, ABySS, IDBA-UD and CABOG, which were found to complement each other in assembling metagenomic sequences. Making a decision of which assembling approaches to use according to the sequencing coverage estimation algorithm for each short read, InteMAP presents an automatic platform suitable to assemble real metagenomic NGS data with uneven coverage distribution of sequencing depth. 12/4/2015 detailed information
InterProScan5.17-56.0LinuxInterProScan is a bioinformatics tool that provides a one-stop-shop for automated sequence analysis of both protein and nucleic acid, the latter via a full six-frame translation. It offers the ability to identify both structural and functional regions of interest, based upon methods and models that have been generated by a large number of member groups ('member databases'). 9/20/20133/23/2016detailed information
javajdk1.8.0_121LinuxJava3/27/20151/24/2017detailed information
jbrowse1.12.1LinuxGenome browser - local instance in BioHPC Lab using Docker3/29/2017 detailed information
jellyfish2.2.3LinuxJellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.10/17/201410/22/2015detailed information
JoinMap4.1WindowsSoftware for the calculation of genetic linkage maps in experimental populations of diploid species 9/11/2014 detailed information
julia0.3.5LinuxJulia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.1/16/2015 detailed information
jupyter4.0.6LinuxThe Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. 2/16/2016 detailed information
kallisto0.42.4LinuxA program for quantifying abundances of transcripts from RNA-Seq data11/2/2015 detailed information
Kent source utilities2009-11-09LinuxUCSC Genome Browser utility programs.3/4/20143/4/2014detailed information
khmer0.4Linuxkhmer is a library and suite of command line tools for working with DNA sequence.5/8/201311/6/2013detailed information
LACHESIS20161130LinuxChromosome-scale scaffolding of de novo genome assemblies using HiC data11/30/2016 detailed information
lcMLkin0LinuxInfer biological relatedness from low coverage 2nd generation sequencing data.4/14/2016 detailed information
LDAK4.9LinuxLDAK – currently the world’s most popular software for obtaining Linkage Disequilibrium Adjusted Kinships8/11/2015 detailed information
leeHomAug_13_2014LinuxRemoves the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. Used for ancient DNA sequences.8/5/2015 detailed information
LINKSv1.8.4LinuxLINKS is a genomics application for scaffolding or re-scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd.12/21/2016 detailed information
LocusZoom1.3LinuxLocusZoom is designed to facilitate viewing of local association results together with useful information about a locus.7/8/2014 detailed information
longranger2.1.2LinuxLong Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.1/25/2017 detailed information
LUCY1.20pLinuxRaw DNA sequence trimming and processing command line tool.12/13/20115/1/2012detailed information
LUCY22.19pLinuxLucy2 is a raw DNA sequence trimming and visualization tool based on the command-line tool Lucy1.1/31/20131/31/2013detailed information
LUMPY0.2.13LinuxStructural variation detection framework 1/13/20147/20/2016detailed information
MACS1.4.2LinuxModel-based Analysis of ChIP-Seq (MACS) on short reads sequencers.12/13/20115/1/2012detailed information
MaCS simulator0.4eLinuxA simulator of the coalescent process that simulates geneologies spatially across chromosomes as a Markovian process.8/16/2016 detailed information
MACS22.1.0LinuxModel-based Analysis of ChIP-Seq (MACS) on short reads sequencers.5/10/20123/23/2016detailed information
MAFFT7.273-with-extensionsLinuxMultiple sequence alignment program 7/23/20143/26/2016detailed information
MAKER2.32LinuxMAKER is an easy-to-configure, portable genome annotation pipeline. MAKER allows smaller eukaryotic genome projects and prokaryotic genome projects to annotate their genomes and to create genome databases.1/23/20132/15/2016detailed information
MAQ0.7.1LinuxMaq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.12/13/20115/2/2012detailed information
MASHv1.1LinuxFast genome and metagenome distance estimation using MinHash7/1/2016 detailed information
MaSuRCA3.2.1LinuxWhole genome assembly of short reads7/18/20141/24/2017detailed information
Mauve2.4.0-2015-02-13LinuxMauve is a software package that attempts to align orthologous and xenologous regions among two or more genome sequences that have undergone both local and large-scale changes.3/24/2015 detailed information
mccortex2016-09-19LinuxPopulation De Novo Assembly and Variant Calling5/22/20149/19/2016detailed information
megahit1.0.3-7-g663eb28LinuxAn ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn11/2/2015 detailed information
MEGAN5.10.0LinuxMetagenomic Analyzer4/2/2015 detailed information
MEME Suite4.11.2_1LinuxMotif-based sequence analysis tools (command line, without web server functionality)7/27/20158/31/2016detailed information
MERLIN1.1.2LinuxMERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around.1/13/2017 detailed information
MetaBATv0.32.4LinuxAn Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities.11/2/2016 detailed information
metaCRISPR20170206LinuxmetaCRISPR is a tool to assemble CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats and Associated Proteins) from metagenomic sequencing data.2/6/2017 detailed information
MetAMOSv1.5rc3LinuxA modular framework for (meta)genomic assembly, analysis and validation.6/11/2014 detailed information
MetaPathways2.5.1LinuxMetaPathways v2.5 is a meta'omic analysis pipeline for the annotation and analysis for environmental sequence information.9/21/2016 detailed information
MetaPhlAn2.0LinuxA computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data4/15/20151/30/2017detailed information
MetaVelvet1.2.02LinuxAn extension of Velvet assembler to de novo metagenome assembly from short sequence reads.6/11/2014 detailed information
MetaVelvet-SL1.0LinuxAn extension of Velvet assembler to de novo metagenomic assembler utilizing supervised learning.6/11/2014 detailed information
Migrate-n3.6.11LinuxMigrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes3/13/2017 detailed information
mira4.0.2LinuxMIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects.6/11/2014 detailed information
miRDeep20.0.5LinuxA tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades.8/21/201212/7/2012detailed information
MISO (misopy)0.4.9LinuxMISO (Mixture-of-Isoforms) 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. 12/17/20131/23/2015detailed information
MixMapper2.0LinuxThe MixMapper software performs admixture inference from allele frequency moment statistics 2/6/20143/26/2016detailed information
MKTest2.0LinuxThis software implements various extensions of the McDonald-Kreitman test, often used to estimate the contribution of positive natural selection to long-term molecular evolution. The software including maximum likelihood methods that allow for formal comparison of different classes of locus. 11/24/2014 detailed information
MMSEQ1.0.0-beta2LinuxA pipeline for obtaining expression estimates from RNA-seq data.2/21/20121/31/2013detailed information
mothur1.38.1LinuxA single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community11/1/2016 detailed information
MrBayes3.2.2LinuxMrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.1/13/20145/30/2014detailed information
mrsFAST3.3.6LinuxmrsFAST is designed to map short reads to reference genome assemblies; in a fast and memory-efficient manner. Mismatches only (no indels).2/19/2015 detailed information
msld20150708LinuxLD stats calculated from ms-like output7/8/2015 detailed information
MSMC2015-09-15Linuxmsmc can infer the scaled population size of a single population as a function of time and the timing and nature of population separations between two populations.5/7/20153/4/2016detailed information
MSR-CA Genome Assembler1.9.4LinuxWhole genome assembly of short reads12/3/20122/13/2013detailed information
msstats0.3.2LinuxReads in data from Hudson's coalescent simulation program ms and calculates several common summary statistcs.9/2/2014 detailed information
MSTMap20140610LinuxMSTMap is a software tool that is capable of constructing genetic linkage maps efficiently and accurately.6/10/2014 detailed information
mugsyv1r2.2Linuxmultiple whole genome aligner11/18/2014 detailed information
MultiQC0.8LinuxA modular tool to aggregate results from bioinformatics analyses across many samples into a single report.12/5/2016 detailed information

359 Records found. Show               


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