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 1.30LinuxFragGeneScan is an application for finding (fragmented) genes in short reads.10/4/2017 detailed information
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
albacore LinuxNanopore base caller.6/2/2017 detailed 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-LG52415LinuxIllumina short reads assembly tool.12/14/20111/9/2018detailed information
AMOS3.1.0LinuxAMOS is a collection of tools and class interfaces for the assembly of DNA reads. 1/12/20131/14/2013detailed information
AMPHORA2LinuxAMPHORA is an Automated Phylogenomic Inference Pipeline for bacterial sequences7/26/20177/27/2017detailed 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
antiSMASH4.02LinuxantiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.12/1/2017 detailed information
apollo20170925LinuxManual genome annotation9/25/2017 detailed information
Arlequin3.5.2.2LinuxAn Integrated Software for Population Genetics Data Analysis10/31/2017 detailed 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
Augustus3.3LinuxAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences1/23/201310/25/2017detailed information
bamtools2.3.0LinuxBAM file processing and filtering.12/13/20113/24/2014detailed information
Basset0.1.0LinuxDeep convolutional neural networks for DNA sequence analysis.5/15/2017 detailed 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
BBmap37.50LinuxThis package includes BBMap, a short read aligner, as well as various other bioinformatic tools.11/6/20159/7/2017detailed information
BCFtools1.3.1Linuxbcftools — utilities for variant calling and manipulating VCFs and BCFs.2/20/2017 detailed information
bcl2fastq2.20.0Linuxbcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.8/7/201711/14/2017detailed information
BCP1.1LinuxBayesian Change-point Model (BCP) is a method for analysis different type of ChIP-seq data.10/23/2017 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
bigWig20171211LinuxR library to work with UCSC bigwig files12/11/2017 detailed 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
Boost1.62.0LinuxBoost provides free peer-reviewed portable C++ source libraries.12/17/201410/25/2017detailed 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
BPGA1.3LinuxComprehensive pan genome analysis of microorganisms10/25/2017 detailed 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
BUSCO3.0.2LinuxAssessing genome assembly and annotation completeness.1/22/201610/25/2017detailed information
BWA0.7.13LinuxBWA is a software package for mapping low-divergent sequences against a large reference genome.12/13/20113/22/2016detailed information
canu1.6Linuxassemble pacbio reads2/11/20168/31/2017detailed information
CAP312/21/07LinuxA DNA Sequence Assembly Program4/4/2014 detailed information
cBar1.2LinuxDistinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data11/1/2017 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
CellRanger2.1.0LinuxA set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.5/15/201711/14/2017detailed information
centrifuge20171218LinuxMicrobial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. 12/18/2017 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
cmake3.6.3LinuxCMake is an open-source, cross-platform family of tools designed to build, test and package software5/22/2017 detailed information
CNVnator0.3LinuxA tool for CNV discovery and genotyping from depth of read mapping6/23/20156/23/2015detailed information
cortex_var1.0.5.21Linuxcortex_var is a tool for genome assembly and variation analysis from sequence data. 7/18/2017 detailed 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
cuda8.0.61LinuxA parallel computing platform and programming model invented by NVIDIA.5/15/2017 detailed information
Cufflinks2.2.1LinuxRNA-seq reference guided transcript assembly, quantification and differential expressed gene identification12/13/20115/6/2014detailed information
cutadapt1.14Linuxcutadapt removes adapter sequences from high-throughput sequencing data.10/11/20138/11/2017detailed 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
dadi-1.6.3_modif1.6.3_modLinuxModified Dadi software6/7/2017 detailed information
dDocent2.2.16Linuxsimple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing.8/29/2017 detailed information
DeconSeq0.4.3LinuxDECONtamination of SEQuence data using a modified version of BWA-SW11/6/2015 detailed information
deepTools2.5.3LinuxA suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data.10/14/201610/18/2017detailed 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
dREG20171211LinuxDetection of Regulatory DNA Sequences using GRO-seq Data.4/28/201612/11/2017detailed information
dREG.HD20171212LinuxThe dREG package uses support vector regression (SVR) to identify active TREs solely from PRO-seq data.12/12/2017 detailed information
Drop-seq1.12LinuxDrop-seq is a technology that allows biologists to analyze genome-wide gene expression in thousands of individual cells in a single experiment. 6/11/2017 detailed information
dropSeqPipe20171014Linuxhis pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab.6/16/201710/14/2017detailed 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
entropy Linuxadmixture proportion and admixture class models9/9/2017 detailed information
ephem3.7.6.0LinuxPython package for performing high-precision astronomy computations12/26/2017 detailed 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
ete33LinuxA Python framework for the analysis and visualization of trees.10/4/2017 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
fastcluster20170926LinuxThis library provides Python functions for hierarchical clustering.9/26/2017 detailed information
FastML20150324LinuxMaximum Likelihood ancestral sequence reconstruction3/24/2015 detailed information
fastp20171214LinuxA tool designed to provide fast all-in-one preprocessing for FastQ files12/14/2017 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
FragGeneScan1.3.0LinuxFragGeneScan is an application for finding (fragmented) genes in short reads.10/4/2017 detailed information
freebayesv1.0.2LinuxBayesian haplotype-based polymorphism discovery and genotyping.5/21/20144/14/2016detailed information
FunGene Pipeline20170826LinuxFunctional Gene Pipeline Scripts contains a set of python scripts that allows to run one or more individual tools offered by RDP FunGene Pipeline8/25/2017 detailed information
GAEMR1.0.1LinuxGAEMR is a complete genome analysis package that helps you evaluate and report on a genome assembly's completeness, correctness, and contiguity.11/8/2017 detailed information
GATK3.8LinuxThe Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data.12/13/201111/1/2017detailed information
GBRS0.1.5LinuxGBRS is a suite of tools for reconstructing genomes using RNA-Seq data from multiparent population and quantifying allele specific expression.9/9/2017 detailed 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
GEMMA0.96LinuxGenome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS). 4/16/20149/28/2017detailed 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
gensim20170920LinuxGensim is a free Python library designed to automatically extract semantic topics from documents, as efficiently (computer-wise) and painlessly (human-wise) as possible.9/20/2017 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 parallel20170522LinuxGNU parallel is a shell tool for executing jobs in parallel using one or more computers.4/22/2016 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
HAPCUT206.17.2017LinuxHapCUT2 is a maximum-li.kelihood-based tool for assembling haplotypes from DNA sequence reads2/26/20176/17/2017detailed 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
HISAT22-2.1.0LinuxHISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads.6/8/20168/18/2017detailed 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
Homer4.9LinuxSoftware for motif discovery and next-gen sequencing analysis5/8/2017 detailed 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
hyperopt20171120LinuxHyperopt is a Python library for serial and parallel optimization over awkward search spaces, which may include real-valued, discrete, and conditional dimensions.11/20/2017 detailed information
HyPhy2.2.7LinuxHyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.2/20/20125/21/2017detailed 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
IgBLAST1.7.0LinuxIgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences.10/6/2017 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
IMa28.27.12LinuxProgram for fitting the Isolation w/ Migration model using a Markov chain Monte Carlo method6/7/2017 detailed information
IMa2p20170907LinuxProgram for fitting the Isolation w/ Migration model using a Markov chain Monte Carlo method. Parallel version.9/7/2017 detailed 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
INDELseek20171005LinuxDetect complex indels from next-generation sequencing reads10/5/2017 detailed information
infernal1.1.2LinuxInfernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities5/11/2017 detailed 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
iRep20170918LinuxiRep is a method for determining replication rates for bacteria from single time point metagenomics sequencing and draft-quality genomes.9/18/2017 detailed 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
jupyter20171218LinuxThe Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. 2/16/201612/18/2017detailed information
kallisto0.42.4LinuxA program for quantifying abundances of transcripts from RNA-Seq data11/2/2015 detailed information
Kent Utilities2017-11-17LinuxUCSC/ENCODE utility programs.3/4/201411/17/2017detailed 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

437 Records found. Show               


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