sci-biology

• ABI-connectivity-data 0.2 1 overlay Connectivity data from the Allen Mouse Brain data portal
• ABI-expression-data 0.2 1 overlay Gene expression data form the Allen Mouse Brain data portal
• ANGLE-bin 20080813-r1 1 overlay CDS prediction overcoming sequencing errors in unfinished cDNA
• AlignGraph 9999 1 overlay Reference-genome-assisted asssembly of contigs/scaffolds using PE reads
• BEP032tools 0.0.1_alpha 1 overlay Conversion and validation tools for BEP 032
• BRAKER 2.1.2 1 overlay Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS
• BRANCH 9999 1 overlay Extend partial transcripts with sequence from other reads or genomic contigs
• CAT 1.3 1 overlay Codon usage bias (composition) and its statistical significance
• FLASH 1.2.11 1 overlay Paired-end mates merge from fragments
• Fastaq 3.18.0 1 overlay Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers
• GAL 0.2.2_p20200508 1 overlay Genome Annotation Library (incl. fasta_tool)
• IMAGE 2.4.1 1 overlay Iterative Mapping and Assembly for Gap Elimination using paired-end Illumina
• KING 2.2.7 1 overlay Check family relationship and infer population structure
• KaKs_Calculator 2.0 1 overlay Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates
• LINKS 2.0.1 1 overlay Scaffold genome assemblies by Chromium/PacBio/Nanopore reads
• MaSuRCA 4.1.0 1 overlay de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore
• MeV 4.8.1 1 overlay Multiple experiment Viewer for genomic data analysis
• MochiView 1.46-r1 1 overlay Genome browser and analysis
• MuSeqBox 5.7.2021 1 overlay Parse and filter BLAST output into tab-delimited file
• NGSEPcore 4.0.3 1 overlay NGSEP (CNV and indel discovery)
• NGSEPcore-bin 4.0.3 1 overlay NGSEP (CNV and indel discovery)
• ONTO-PERL 1.45 1 overlay Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)
• ParaAT 1.0 1 overlay Create multiple protein-coding DNA alignments and back-Translation
• RAILS 1.5.1 1 overlay Cobbler and RAILS scaffolding tools acting on SAM streams
• Rcorrector 1.0.4 1 overlay Error correction for Illumina RNA-seq reads
• SEECER 0.1.3-r3 1 overlay SEquence Error Corrector for RNA-Seq reads
• SPAdes 3.15.5 1 overlay De novo de Bruijn genome assembler overcoming uneven coverage
• SSAKE 3.8.2 1 overlay Short-read trimmer, OLC assembler, scaffolder in PERL using the 3'-most k-mers
• STAR 2.7.10a ::gentoo 1 overlay STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays
• SnpEff 4.3t 1 overlay SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF
• SolexaQA 3.1.7.1 1 overlay Analyze and trim single-end and paired-end reads, show quality statistics
• TransDecoder 5.5.0 1 overlay Extract ORF/CDS regions from FASTA sequences
• VarScan 2.4.4 1 overlay Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)
• VarScan-bin 2.4.4 1 overlay Variant detection (germline, multi-sample, somatic mut., CNA), SNP
• VelvetOptimiser 2.2.6 1 overlay Optimise Velvet sequence assembler
• YASRA 2.33 1 overlay Yet Another Short Read Assembler aligning to a reference using LASTZ
• aaindex 9.1-r2 ::gentoo 1 overlay Amino acid indices and similarity matrices
• abacas 1.3.1 1 overlay Order and orientate DNA contigs even via 6-frame protein alignments
• abyss 2.3.4 ::gentoo 1 overlay Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
• act-bin 17.0.1 1 overlay DNA contig sequence comparison tool supplementing Artemis
• afni 24.1.16 19 mo 2 overlays Advanced Normalitazion Tools for neuroimaging
• afni-datasets 20240503 1 overlay Datasets for using and testing sci-biology/afni
• aghermann 1.1.2-r2 1 overlay A sleep-research experiment manager, EDF viewer & Process S simulator
• align_to_scf 1.06 1 overlay View trace information at a given position missing from Roche .ace files
• amap 2.2-r6 ::gentoo 1 overlay Protein multiple-alignment-based sequence annealing
• angsd 0.933 1 overlay Population genetics analysis package
• assembly-stats 9999 1 overlay Assembly statistics (min, max, sum, N50, N90, count gaps and Ns)
• augustus 3.5.0 ::gentoo 1 overlay Eukaryotic gene predictor
• bam-readcount 0.8.0 1 overlay Count DNA sequence reads in BAM files and other statistics calculations
• bambus 2.33-r2 1 overlay Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle
• bamql 1.6.1 1 overlay Extract reads from BAM files
• bamstats 0.4 6 mo 1 overlay A program to extract various information from BAM alignment files
• bamtools 2.5.3 ::gentoo 1 overlay A programmer's API and an end-user's toolkit for handling BAM files
• barrnap 0.9 1 overlay Predict Bacterial and Archaeal rRNA genes and output in GFF3 format
• bcftools 1.23.1 ::gentoo 1 overlay Utilities for variant calling and manipulating VCF and BCF files
• beagle 5.1 1 overlay Genotype calling/phasing, imputation of ungenotyped markers
• bedops 2.4.39 1 overlay Manipulate BED file (alternative to bedtools)
• bedtools 2.31.1 ::gentoo 1 overlay Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats
• bfast 0.7.0a-r1 ::gentoo 1 overlay Blat-like Fast Accurate Search Tool
• bids-cli 0.0.1 19 mo 1 overlay BIDS Command Line Interface
• bids-schema 1.7.0_p20220217 19 mo 1 overlay YAML schema reference for BIDS specification
• bidsschematools 0.7.1 19 mo 2 overlays A Python library for working with the BIDS schema
• biobambam2 2.0.146 1 overlay Tools for bam file processing (libmaus2)
• biogrep 1.0-r3 ::gentoo 1 overlay Multithreaded tool for matching large sets of patterns against biosequence DBs
• bioperl 1.6.9-r1 ::gentoo 1 overlay Perl tools for bioinformatics - Core modules
• bioperl-db 1.6.9-r2 ::gentoo 1 overlay Perl tools for bioinformatics - Perl API that accesses the BioSQL schema
• bioperl-network 1.6.9-r1 ::gentoo 1 overlay Perl tools for bioinformatics - Analysis of protein-protein interaction networks
• bioperl-run 1.6.9-r1 ::gentoo 1 overlay Perl wrapper modules for key bioinformatics applications
• biopython 1.87 ::gentoo 1 overlay Python modules for computational molecular biology
• biosql 1.0.1-r2 ::gentoo 1 overlay A generic bioinformatics relational database model
• bismark 0.23.0 1 overlay Map bisulfite converted sequence reads and cytosine methylation states
• blat 34-r3 ::gentoo 1 overlay The BLAST-Like Alignment Tool, a fast genomic sequence aligner
• bowtie 2.5.1 ::gentoo 1 overlay Popular short read aligner for Next-generation sequencing data
• brat 1.2.4 1 overlay Bisulfite-treated Reads Analysis Tool (short read mapper)
• brat_bw 2.0.1 1 overlay Bisulfite-aware short read mapper, FM-index, no InDel support
• brat_nova 20160103 1 overlay Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align
• brkraw 0.3.11 1 overlay Fast and easy statistical learning on NeuroImaging data
• bru2nii 1.0.20180303 1 overlay Converts Bruker ParaVision MRI data to the NIfTI file format
• btl_bloomfilter 1.2.1 1 overlay BTL C/C common bloom filters
• bwa 0.7.17 ::gentoo 1 overlay Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner
• bx-python 0.14.0 1 overlay Library for rapid implementation of genome scale analyses
• cast-bin 20080813 1 overlay Predict low-complexity regions in putative proteins
• cd-hit 4.6.6-r1 ::gentoo 1 overlay Clustering Database at High Identity with Tolerance
• cdbfasta 0.1 1 overlay FASTA record indexing/retrievieng utility
• cellblender 1.0.1 2 yr 1 overlay MCell blender addon. Create, Simulate, Visualize, and Analyze 3D Cell Models
• clustal-omega 1.2.4-r1 ::gentoo 1 overlay Scalable multiple alignment of protein sequences
• clustalw 2.1-r2 ::gentoo 1 overlay General purpose multiple alignment program for DNA and proteins
• clustalw-mpi 0.13-r3 ::gentoo 1 overlay An MPI implemention of the ClustalW general purpose multiple alignment algorithm
• cluster 1.59 1 overlay Hierarchical, k-means, k-medians clustering for expression/microarray analysis
• cmdock 0.2.0-r3 1 overlay Program for docking ligands to proteins and nucleic acids
• cnrun 2.1.0-r2 1 overlay A NeuroML-enabled, precise but slow neuronal network simulator
• codonw 1.4.4-r2 1 overlay Multivariate statistical analysis of codon and amino acid usage
• conform-gt 1174 1 overlay Modify your Variant Call Format file to be consistent with reference VCF
• coral 1.4.1 1 overlay Error corrector for Illumina and Roche/454 reads using multiple alignment info
• cross_genome 20140822 1 overlay Genome scaffolding using cross-species synteny
• cutadapt 4.9 1 overlay Adapter trimming and other preprocessing of high-throughput sequencing reads
• cutg 160-r1 ::gentoo 1 overlay Codon usage tables calculated from GenBank
• cytoscape-bin 3.10.4 1 overlay A visualization platform for molecular interaction networks
• dargcc_bidsdata 1.0 1 overlay BIDS data selection of wildtype animals from DARGCC article
• dcm2niix 1.0.20210317 1 overlay DICOM to NIfTI converter
• dcmstack 0.9 1 overlay DICOM to Nifti coversion
• deeptools 3.5.6 1 overlay Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig
• deeptools-intervals 0.1.9-r1 1 overlay Constructing interval trees with associated exon/annotation information
• dialign-tx 1.0.2-r2 ::gentoo 1 overlay Greedy and progressive approaches for segment-based multiple sequence alignment
• dialign2 2.2.1-r1 ::gentoo 1 overlay Multiple sequence alignment
• diamond 2.0.6 1 overlay Alternative of blastp/blastx searches using DNA short reads through protein db
• dipy 1.1.1-r1 1 overlay Computational neuroanatomy project focusing on diffusion MRI
• drlfom_bidsdata 1.1.1 19 mo 2 overlays BIDS data files released with the DRLFOM publication
• edena 3.131028 1 overlay De novo short read OLC assembler (overlap-layout-consensus)
• elph 1.0.1-r3 ::gentoo 1 overlay Estimated Locations of Pattern Hits - Motif finder program
• embassy 6.6.0-r3 ::gentoo 1 overlay A meta-package for installing all EMBASSY packages (EMBOSS add-ons)
• embassy-cbstools 1.0.0.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Applications from the CBS group
• embassy-clustalomega 1.1.0.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment
• embassy-domainatrix 0.1.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Protein domain analysis add-on package
• embassy-domalign 0.1.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Protein domain alignment add-on package
• embassy-domsearch 0.1.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Protein domain search add-on package
• embassy-emnu 1.05.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Simple menu of EMBOSS applications
• embassy-esim4 1.0.0.660-r1 ::gentoo 1 overlay EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA
• embassy-hmmer 2.3.2.660-r1 ::gentoo 1 overlay EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs
• embassy-iprscan 4.3.1.660-r1 ::gentoo 1 overlay EMBOSS integrated version of InterProScan motif detection add-on package
• embassy-mse 3.0.0.660-r1 ::gentoo 1 overlay EMBOSS integrated version of MSE - Multiple Sequence Screen Editor
• embassy-phylipnew 3.69.660-r1 ::gentoo 1 overlay EMBOSS integrated version of The Phylogeny Inference Package
• embassy-signature 0.1.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Protein signature add-on package
• embassy-structure 0.1.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Protein structure add-on package
• embassy-topo 2.0.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Transmembrane protein display
• embassy-vienna 1.7.2.660-r1 ::gentoo 1 overlay EMBOSS integrated version of Vienna RNA package - RNA folding
• emboss 6.6.0-r4 ::gentoo 1 overlay The European Molecular Biology Open Software Suite - A sequence analysis package
• epga 9999 1 overlay De novo assembler using distribution of reads and insert size
• erpin 5.5b 1 overlay Easy RNA Profile IdentificatioN, an RNA motif search program
• eugene 4.1d-r1 ::gentoo 1 overlay Prokaryotic and Eukaryotic gene predictor
• exonerate 2.2.0-r3 ::gentoo 1 overlay Generic tool for pairwise sequence comparison
• exonerate-gff3 9999 1 overlay exonerate-2.2.0 with patches to add GFF3 formatted output
• fasta 36.3.8i-r1 ::gentoo 1 overlay FASTA is a DNA and Protein sequence alignment software package
• fastdnaml 1.2.2_p10 1 overlay Maximum likelihood phylogenetic tree builder for DNA sequences
• fastp 1.3.6 1 overlay An ultra-fast all-in-one FASTQ preprocessor
• fastqc 0.11.9 1 overlay Quality control FASTA/FASTQ sequence files
• fasttree 2.1.11 ::gentoo 1 overlay Fast inference of approximately-maximum-likelihood phylogenetic trees
• fastx_toolkit 0.0.14-r1 ::gentoo 1 overlay Tools for Short Read FASTA/FASTQ file processing
• ffindex 1.0 1 overlay Simple index/database for huge amounts of small files
• finchtv 1.3.1-r3 ::gentoo 1 overlay Graphical viewer for chromatogram files
• flexbar 3.5.0 1 overlay Barcode, MID tag and adapter sequence removal
• flowsim 0.3.5 6 mo 1 overlay Simulate 454 pyrosequencing
• foldingathome 8.5.6 14 d ::gentoo 2 overlays Folding@Home is a distributed computing project for protein folding
• freebayes 1.3.5 1 overlay Bayesian gen. variant detector to find short polymorphisms
• fsa 1.15.9 1 overlay Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot
• fsl 6.0.5 1 overlay Analysis of functional, structural, and diffusion MRI brain imaging data
• geneathome 1.10-r5 1 overlay BOINC application for expanding Gene Regulatory Networks (GRN)
• genepop 4.7 1 overlay Population genetics analysis
• genomeview-bin 2450-r1 1 overlay Genome browser and annotation tool
• germline 1.5.3 1 overlay Find shared segments of Identity by Descent (IBD) between pairs of individuals
• gffcompare 0.12.2 1 overlay Compare, classify, merge, track, annotate GFF files
• gffread 0.12.7 1 overlay GFF/GTF utility providing format conversions, filter/extract regions from FASTA
• gffutils 0.14 1 overlay GFF and GTF file manipulation and interconversion
• glean 1.0.1 1 overlay Merge various gene prediction into one (unsupervised learning system)
• glimmer 3.02b ::gentoo 1 overlay An HMM-based microbial gene finding system from TIGR
• glimmerhmm 3.0.4 ::gentoo 1 overlay A eukaryotic gene finding system from TIGR
• gmap 2020.10.27 ::gentoo 1 overlay A Genomic Mapping and Alignment Program for mRNA and EST Sequences
• gnaural 1.0.20080808 22 mo 1 overlay A programmable binaural-beat generator, implementing the principle of binaural beats as described in the October 1973 Scientific American article "Auditory Beats in the Brain" (Gerald Oster).
• grabix 9999 1 overlay Provide random access to text files BGZF compressed with bgzip
• graf-bin 2.4 1 overlay Find closely related subjects using SNP genotype data, validate pedigree file
• grappa 2.0 1 overlay Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
• hexamer 19990330 1 overlay Predict CDS using 6mers without deriving information from base composition
• hisat2 2.2.1 1 overlay Align DNA reads to a population of genomes
• hmmer 3.1_beta2-r1 ::gentoo 1 overlay Sequence analysis using profile hidden Markov models
• idba 1.1.3 1 overlay De novo De Bruijn graph assembler iteratively using multimple k-mers
• iedera 1.05-r2 ::gentoo 1 overlay Subset seed design tool for DNA sequence alignment
• imagej 1.54i-r1 1 overlay Image Processing and Analysis in Java
• infernal 1.0.2-r1 ::gentoo 1 overlay Inference of RNA alignments
• iqpnni 3.3.2-r2 ::gentoo 1 overlay Important Quartet Puzzling and NNI Operation
• irsabi_bidsdata 1.4 1 overlay BIDS data files released with the IRSABI publication
• irsabi_brudata 1.4.1 19 mo 1 overlay Raw data files released with the IRSABI publication
• jalview-bin 2.11.5.1 1 overlay Editor of multiple sequence alignments.
• jannovar-bin 0.35 1 overlay Exome annotation tool (upstream jar binaries)
• jellyfish 2.3.0 1 overlay k-mer counter within reads for assemblies
• jtreeview-bin 1.2.0 1 overlay Viewer for Microarray Data in PCL or CDT formats
• kalign 2.03-r3 ::gentoo 1 overlay Global and progressive multiple sequence alignment
• kallisto 0.46.2-r1 ::gentoo 1 overlay Near-optimal RNA-Seq quantification
• karect 1.0 1 overlay Error-correct mismatches and InDels of raw reads incl. paired-end
• lagan 2.0-r4 ::gentoo 1 overlay The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA
• lastz 1.04.03 1 overlay A pairwise DNA sequence aligner, a BLASTZ replacement
• lemur-brain-atlas 0.1 1 overlay MRI Brain Template and Atlas of the Mouse Lemur
• libBigWig 0.4.7 1 overlay C library for handling bigWig files (functionally replacing Jim Kent's lib)
• libgtextutils 0.6.1-r1 ::gentoo 1 overlay Gordon Text utils Library
• lighter 1.1.2 1 overlay NGS reads corrector
• lucy 1.20 1 overlay DNA sequence quality and vector trimming tool
• lumpy-sv 0.3.1 1 overlay Probabilistic framework for structural variant discovery
• mafft 7.525 ::gentoo 1 overlay Multiple sequence alignments using a variety of algorithms
• mappy 2.26 1 overlay Minimap2 python binding
• maq 0.7.1-r4 ::gentoo 1 overlay Mapping and Assembly with Qualities, mapping NGS reads to reference genomes
• maqview 0.2.5-r5 ::gentoo 1 overlay GUI for sci-biology/maq, a short read mapping assembler
• mcell 3.3 2 yr 1 overlay MCell: Monte Carlo Simulator of Cellular Microphysiology
• megahit 1.2.9 1 overlay Metagenome assembler using succinct de Bruijn graph approach with CUDA
• merlin 1.1.2 1 overlay Statistical analysis of gene flow in pedigrees
• mfold_util 4.7-r1 21 mo 1 overlay mfold_util: graphic rendering for UNAFold
• minimap2 2.24-r1 1 overlay splice-aware sequence aligner with SSE2 and SSE4.1
• mip-scaffolder 0.6 1 overlay Scaffold contigs using ABI Solid or Illumina mate pair info
• miranda 3.3a 1 overlay An algorithm for finding genomic targets for microRNAs
• mmseqs2 13.0-r1 1 overlay Fast and sensitive sequence search and clustering
• mosaik 2.2.30 ::gentoo 1 overlay A reference-guided aligner for next-generation sequencing technologies
• mothur 1.48.2 ::gentoo 1 overlay Suite of algorithms for ecological bioinformatics
• mouse-brain-templates 0.5.3 1 overlay A collection of mouse brain templates in NIfTI format
• mrbayes 3.2.7 ::gentoo 1 overlay Bayesian Inference of Phylogeny
• mreps 2.6.01 1 overlay Identification of serial/tandem repeats in DNA sequences
• mrfast 2.6.0.1 1 overlay Micro Read Fast Alignment Search Tool
• msautil 1.1-r1 1 overlay Reformat/edit FASTA files and compute simple statistics (N50, quartiles, mode)
• multiqc 1.33 1 overlay Aggregate bioinformatics results across many samples into a single report
• mummer 3.23-r1 ::gentoo 1 overlay A rapid whole genome aligner
• muscle 5.1.0 ::gentoo 1 overlay Multiple sequence comparison by log-expectation
• nanopolish 9999 1 overlay Signal-level analysis of Oxford Nanopore sequencing data
• neuroconv 0.4.8-r1 19 mo 2 overlays Create NWB files from proprietary formats.
• newick-utils 1.6-r3 ::gentoo 1 overlay Tools for processing phylogenetic trees
• nextclip 1.3.1 1 overlay Split Illumina Nextera long mate-pairs
• nitime 0.10.2 1 overlay Time-series analysis of neuroscience data
• nrcl 110625 1 overlay Containment clustering and layout utility for processing pairwise alignments
• ntCard 1.2.2 1 overlay Estimate k-mer coverage histogram of genomics data
• nvcz_data 0.2 19 mo 1 overlay Bruker and BIDS data from neurovascular coupling experiments
• nvcz_preprocessed 1.0.0 19 mo 1 overlay SAMRI-preprocessed data in BIDS fromat from the NVCZ study
• nxtrim 0.4.3 1 overlay Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker
• open-ephys-gui 0.6.7 1 overlay Processing, recording, and visualizing multichannel ephys data
• opfvta_bidsdata 2.1 19 mo 2 overlays BIDS data files released with the OPFVTA publication
• opfvta_brudata 2.0 19 mo 1 overlay BIDS data files released with the OPFVTA publication
• pairagon 1.1 1 overlay HMM-based cDNA to genome aligner
• pals 1.0-r2 ::gentoo 1 overlay Pairwise Aligner for Long Sequences
• paml 4.10.10 ::gentoo 1 overlay Phylogenetic Analysis by Maximum Likelihood
• parafly 0.1.0 1 overlay Parallel cmd processing utility
• pbbam 2.1.0 1 overlay PacBio modified BAM file format
• pbcopper 1.9.5 1 overlay Core C++ library for data structures, algorithms, and utilities
• perga 9999 1 overlay Paired End Reads Guided Assembler
• perlprimer 1.1.21 1 overlay Primers design for standard PCR, bisulphite PCR and Real-time PCR
• phylip 3.698 ::gentoo 1 overlay The PHYLogeny Inference Package
• phyml 2.4.5-r4 ::gentoo 1 overlay Estimation of large phylogenies by maximum likelihood
• piler 1.0-r2 ::gentoo 1 overlay Analysis of repetitive DNA found in genome sequences
• pilercr 1.0-r3 ::gentoo 1 overlay Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
• pileup 0.6 1 overlay SSAHA2-based pipeline to align reads
• plamri_brudata 0.1 19 mo 1 overlay Bruker ParaVision data files for testing the PlaMRI package
• plink 1.90_pre140514 ::gentoo 1 overlay Whole genome association analysis toolset
• poa 2-r1 ::gentoo 1 overlay Fast multiple sequence alignments using partial-order graphs
• portrait 1.1 1 overlay Ab initio ncRNA prediction
• prank 140603-r1 ::gentoo 1 overlay Probabilistic Alignment Kit
• primer3 2.3.7-r1 ::gentoo 1 overlay Primer Design for PCR reactions
• prinseq-lite 0.20.4 1 overlay Describe, trim, reformat and convert to or form FASTA/FASTQ files
• prints 39.0-r2 ::gentoo 1 overlay A protein motif fingerprint database
• probcons 1.12-r1 ::gentoo 1 overlay Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
• proda 1.0 1 overlay Multiple alignment of protein sequences with repeated and shuffled elements
• prodigal 2.6.3-r1 ::gentoo 1 overlay Prokaryotic Dynamic Programming Genefinding Algorithm
• profphd 1.0.40 ::gentoo 1 overlay Secondary structure and solvent accessibility predictor
• prosite 2017.02-r1 ::gentoo 1 overlay A protein families and domains database
• psx 0.1 1 overlay parallel multi-FASTA file processing tool from TIGR Gene Indices project tools
• pysam 0.24.0 ::gentoo 1 overlay Python interface for the SAM/BAM sequence alignment and mapping format
• quicktree 2.5 1 overlay Rapid reconstruction of phylogenies by the Neighbor-Joining method
• rat-brain-templates 0.2 1 overlay A collection of rat brain templates in NIfTI format
• raxml 8.2.13 ::gentoo 1 overlay Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
• rebase 1901-r2 ::gentoo 1 overlay A restriction enzyme database
• recon 1.08-r1 ::gentoo 1 overlay Automated de novo identification of repeat families from genomic sequences
• rnaplex 0.2 1 overlay RNA-RNA interaction search
• roiextractors 0.5.1 1 overlay Optical imaging data handling from several file formats
• sabre 9999 1 overlay Barcode demultiplexing and trimming tool for Illumina FastQ files
• samri_bidsdata 0.3 1 overlay BIDS-formatted example mouse brain data for SAMRI
• samri_bindata 0.4 1 overlay ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI
• samstat 1.5.1 1 overlay Statistics of BAM/SAM files
• samtools 1.23.1 ::gentoo 1 overlay Utilities for analysing and manipulating the SAM/BAM alignment formats
• scan_for_matches 20121220 1 overlay Pattern search through DNA sequences (aka patscan)
• scythe 9999 1 overlay Bayesian 3'-end adapter (only) trimmer for Illumina/Solexa
• seaview 4.6-r2 ::gentoo 1 overlay A graphical multiple sequence alignment editor
• seqan 3.1.0 ::gentoo 1 overlay C++ Sequence Analysis Library
• seqtk 1.3 1 overlay Manipulate FASTA and FASTQ files
• seqtools 4.44.1 1 overlay Display alignments and GFF files, matrix dot plots (blixem, dotter, belvu)
• sff_dump 1.04 1 overlay Convert Roche SFF files to FASTA file format
• sibsim4 0.20 ::gentoo 1 overlay A rewrite and improvement upon sim4, a DNA-mRNA aligner
• sickle 1.33 1 overlay Windowed adaptive quality-based trimming tool for FASTQ data
• sim4 20030921-r2 ::gentoo 1 overlay A program to align cDNA and genomic DNA
• skewer-bin 0.2.2 1 overlay Adaptor and MID removal / trimming tool
• smalt 0.7.6 1 overlay DNA read mapper using k=20 (successor of ssaha2)
• smalt-bin 0.7.6 1 overlay Pairwise sequence alignment mapping DNA reads onto genomic reference
• snap 20131129 1 overlay HMM-based prokaryotic and eukaryotic gene prediction tool
• snapgene 8.2.2 1 overlay Software for plasmid mapping, primer design, and restriction site analysis
• snpomatic 1.0 1 overlay Stringent short-read aligner supporting filters and various output formats
• spm 12_p7771 1 overlay Analysis of brain imaging data sequences for Octave or Matlab
• sra-tools 2.11.3 1 overlay NCBI Sequence Read Archive (SRA) sratoolkit
• ssaha2-bin 2.5.5-r1 1 overlay SSAHA2: Sequence Search and Alignment by Hashing Algorithm
• stacks 2.60 1 overlay Analyze restriction enzyme data, draw gen. maps, population genomics
• stride 20060723 ::gentoo 1 overlay Protein secondary structure assignment from atomic coordinates
• stringtie 2.1.5 1 overlay Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks
• structure 2.3.4 6 mo 1 overlay Package for using multi-locus genotype data to investigate population structure
• subread 2.0.3 1 overlay NGS suite for analysis of mapped reads, summary of exon/intron/gene counts
• swissknife 1.80 1 overlay Perl library of modules to manipulate SwissProt flatfiles
• t-coffee 11.00-r3 ::gentoo 1 overlay A multiple sequence alignment package
• tabixpp 1.1.0 1 overlay C++ wrapper to tabix indexer
• tagdust 20101028 1 overlay Trim multimers of various primers/adapter from Illumina datasets
• tigr-foundation-libs 2.0-r2 1 overlay TIGR Foundation for C++
• tree-puzzle 5.2-r1 ::gentoo 1 overlay Maximum likelihood analysis for nucleotide, amino acid, and two-state data
• treeviewx 0.5.1.20100823_p4-r1 ::gentoo 1 overlay A phylogenetic tree viewer
• trf 4.04-r2 ::gentoo 1 overlay Tandem Repeats Finder
• trf-bin 4.09 1 overlay Tandem Repeats Finder
• trimmomatic 0.39 1 overlay Illumina adapter trimming tool
• trinityrnaseq 2.13.2 1 overlay Transcriptome assembler for RNA-seq reads
• trnascan-se 1.31-r3 ::gentoo 1 overlay tRNA detection in large-scale genome sequences
• twinscan 4.1.2-r1 1 overlay iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline
• uchime 4.2.40-r1 ::gentoo 1 overlay Fast, accurate chimera detection
• ucsc-genome-browser 260-r2 ::gentoo 1 overlay The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath
• ugene 40.1-r1 1 overlay A free open-source cross-platform bioinformatics software
• unafold 3.8-r3 21 mo ::gentoo 2 overlays Unified Nucleic Acid Folding and hybridization package
• update-blastdb 12.0.0 ::gentoo 1 overlay update_blastdb.pl for local blast db maintainance
• vague-bin 1.0.5 1 overlay GUI for Velvet de novo assembler
• vcflib 1.0.3 1 overlay VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)
• vcftools 0.1.16 ::gentoo 1 overlay Tools for working with VCF (Variant Call Format) files
• velvet 1.2.10 ::gentoo 1 overlay A sequence assembler for very short reads
• verifyBamID 1.1.3 1 overlay Verify sample identity/mix and genotype concordance
• vt 9999 1 overlay A tool set for short variant discovery in genetic sequence data
• wgs_tools 9999 1 overlay Scripts for ncbi-tools++ and SRA postprocessing using taxonomy
• wise 2.4.0_alpha-r1 ::gentoo 1 overlay Intelligent algorithms for DNA searches
• yaha 9999 1 overlay DNA mapper for single-end reads to detect structural variants (SV)
• yass 1.14-r4 ::gentoo 1 overlay Genomic similarity search with multiple transition constrained spaced seeds
• zmap 2.12.0 1 overlay A desktop genome browser using GFF inputs
• zmsort 110625 1 overlay Merge-sort utility for compressed alignment files, with multi-file output
• ztau_bidsdata 1.0 19 mo 1 overlay BIDS data files released with the OPFVTA publication