Software

3D de novo assembly (3D-DNA) pipeline.

BRAKER(1,2,3) is a tool for fully automated genome annotation with GeneMark-ET and AUGUSTUS

Falcon: a set of tools for fast aligning long reads for consensus and assembly

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available.

An interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.

Efficient phylogenomic software by maximum likelihood

Detecting intron retention from RNA-Seq experiments

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library.

A Fast, Accurate, and User-Friendly Ortholog-Finding Algorithm

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.

KmerGenie estimates the best k-mer length for genome de novo assembly.

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

KrakenUniq (formerly KrakenHLL) is a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset.

LAST finds similar regions between sequences.

A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically.

LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.

LDhelmet performs statistical inference for fine-scale variable recombination rate estimation.

Protein Subcelullar Localization Sequenced-Based Predictor

LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.

 LR_Gapcloser is a gap closing tool using uncorrected or corrected long reads generated from Pacbio platform or Nanopore platform. 

TGS scaffolding . Improving draft genomes using long noisy reads.

MACH is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Model-based Analysis of ChIP-Seq

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

This is a version of ALDER (http://groups.csail.mit.edu/cb/alder/) that has been modified to allow multiple admixture events.

MALT (MEGAN alignment tool) is an extension of MEGAN (metagenome analyzer).
MALT performs alignment of metagenomic reads against a database of reference sequences (such as NR, GenBank or Silva) and produces a MEGAN RMA file as output. The software is currently under development.

tracking and quantifying damage patterns in ancient DNA sequences.

MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454)

MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

This program is designed to call m6A from nanopore data using the differences between measured and expected currents.

MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads.

A tool to merge assembled contigs, long reads from metagenomic sequencing runs

MEtaGenome ANalyzer : Metagenomic data analysis : taxonomic and functionnal (SEED and KEGG classification) analysis. 

The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/ONT) metagenomic datasets. It simultaenously carries out read assignment and sample composition estimation. It is faster than classical exact alignment-based approaches, and its output is more information-rich than that of kmer-spectra-based methods. For example, each MetaMaps alignment comes with an approximate alignment location, an estimated alignment identity and a mapping quality.

MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the command-line and was derived from CRT

Ultrafast de novo assembly for long noisy reads (though having no consensus step).

Whole genome shotgun and EST sequence assembler for Sanger, 454, and Solexa / Illumina.

miRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples. Last, a new module for preprocessing of raw Illumina sequencing data produces files for downstream analysis with the miRDeep2 or quantifier module.

This tool counts the number of reads (produced by RNA-Seq) per gene, much like HTSeq-count and featureCounts. The main difference with other tools is that multi-mapping reads are counted differently: if a read is mapped to gene A, gene B, and gene C, the tool will create a new feature, "geneA--geneB--geneC", that will be counted once.

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge proteins/nucleotide sequence sets.

Mobster is used to detect novel (non-reference) Mobile Element Insertion (MEI) events in BAM files and uses both a discordant read pair method and a split-read method.

ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.

MOSAIK is a reference-guided assembler comprising of two main modular programs

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome. mean per-window depth given a window size--as would be used for CNV calling. the mean per-region given a BED file of regions. a distribution of proportion of bases covered at or above a given threshhold for each chromosome and genome-wide. quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20) threshold output to indicate how many bases in each region are covered at the given thresholds. when appropriate, the output files are bgzipped and indexed for ease of use.

The one-stop source for your computational microbial ecology needs. mothur offers the ability to go from raw sequences to the generation of visualization tools to describe alpha and beta diversity.

MrBayes 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.

This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data

A program for the efficient computation of a number of population genetics summary statistics. msums can read ms-format data on (nearly) arbitrary numbers of populations.

Aggregate results from bioinformatics analyses across many samples into a single report.

NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Compare multiple runs of long read sequencing data and alignments.

Filtering and trimming of Oxford Nanopore sequencing data

Plotting tool for Oxford Nanopore sequencing data and alignments.

A nanopore consensus algorithm using a signal-level hidden Markov model. Signal-level algorithms for MinION data.

NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology.

NaS is a hybrid approach developed to take advantage of data generated using MinION device. It combines Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads

Similarity search against databanks.

Similarity search against databanks.

Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche diagnostic.

The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees. We distribute the package under the BSD License. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).

This module provide access to workflows nf-core, there are automatically downloaded into your home.

More info at nf-core/config page.

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations SV detection from paired end reads mapping

NgsRelate can be used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.

NOVOPlasty is a de novo assembler and variance caller for short circular genomes.

Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI for Molecular Genomics) and Daniel Zerbino (previously at the European Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).

Oases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.

OBITools is a set of python programs developed to simplify the manipulation of sequence files in our labs. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.

An alignment tool for optical mapping data.

ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore fast5 file format.

The ORGanelle ASseMbler aims to target the assembling of small sequences over-represented in a whole genome shotgun sequence dataset.

a tool for high speed estimation of homology relations within and between species in massive data sets. orthAgogue is easy to use and offers flexibility through a range of optional parameters.

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification.

The PALEOMIX pipeline is a set of free and open-source pipelines and tools designed to enable the rapid processing of Next Generation Sequencing (NGS) data, starting from de-multiplexed reads from one or more samples, through sequence processing and alignment, and ending with genotyping, phylogenetic inference on the samples, as well as metagenomic analysis of the samples.

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.

PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

PASTA estimates alignments and ML trees from unaligned sequences using an iterative approach. In each iteration, it first estimates a multiple sequence alignment using the current tree as a guide and then estimates an ML tree on (a masked version of) the alignment.

PCAdmix is a method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes.  The method considers data chromosome by chromosome.

Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuraccy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus.

PHASE is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.

The Phi Test is a simple, rapid, and statistically efficient test for recombination.

PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. The pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations.

PhyML is a phylogeny software based on the maximum-likelihood principle.

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

Pilon is an automated genome assembly improvement and variant detection tool.

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

A model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data.

pong is a freely available software package, released by Behr et al. (2016, Bioinformatics), for post-processing output from clustering inference using population genetic data.

Population-scale detection of novel-sequence insertions.

Porechop_abi (ab initio) is an extension of Porechop that is able to infer the adapter sequence from the Oxford Nanopore reads. It discovers the adapter sequence from the reads using approximate k-mers and assembly, and add the sequence found to the adapter list (adapters.py file).

The pp-popularity-contest package sets up a cron job that periodically submits the developers anonymous statistics on the usage of Rost Lab prediction methods installed on this system.

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.

Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction").

PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.

Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

This software package infers population size history from a diploid sequence
using the Pairwise Sequentially Markovian Coalescent (PSMC) model.

Pipeline to help with curating heterozygous diploid genome assemblies (for instance when assembling using FALCON or FALCON-unzip).

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

This module provides a low-level Python wrapper around the Slurm C-API using Cython.

QIIME (pronounced "chime") stands for Quantitative Insights Into ttMicrobial Ecology. QIIME is an open source software package for ttcomparison and analysis of microbial communities, primarily based on tthigh-throughput amplicon sequencing data (such as SSU rRNA) generated tton a variety of platforms, but also supporting analysis of other types ttof data (such as shotgun metagenomic data). QIIME takes users from tttheir raw sequencing output through initial analyses such as OTU ttpicking, taxonomic assignment, and construction of phylogenetic trees ttfrom representative sequences of OTUs, and through downstream ttstatistical analysis, visualization, and production of ttpublication-quality graphics. QIIME has been applied to single studies ttbased on billions of sequences from thousands of samples. ttttt

QmRLFS-finder, the first R-loop finding tool which uses (unsupervised) QmRLFS (Quantitative Models of RLFS) models to predict RLFSs. This command line tool generates locations and detailed information of RLFSs as well as standards-compliant output files for further analysis and visualization.

QUAST evaluates genome assemblies by computing various metrics

QuorUM (Quality Optimized Reads from the University of Maryland) is an error corrector for Illumina reads. 

Ra is as a fast and easy to use assembler for raw reads generated by third generation sequencing.

Consensus module for raw de novo DNA assembly of long uncorrected reads.

Analysis of RAD-seq data for InterSpecific phylogeny

A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.

RAiSD (Raised Accuracy in Sweep Detection) is a stand-alone software implementation of the μ statistic for selective sweep detection.

The software compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences..

RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

RepeatMasker is a program that screens DNA sequences for interspersed repeats (thanks to RepBase repeats databanks specially formatted) and low complexity DNA sequences.

RepeatModeler is a de-novo repeat family identification and modeling package.

The REPET package (t Flutre et al, 2011 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale.

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.

A discriminative method for local ancestry inference

RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.

MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns.

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data

A barcode demultiplexing and trimming tool for FastQ files.

A tool to scaffold long read assemblies with Hi-C data

samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.

SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files.

A tool for assessing the library saturation without any reference genome. .

sbt is a build tool for Scala, Java, and more.

A coalescent simulator for genome-scale sequences.

Segmental Duplication Assembler

SEDEF is a quick tool to find all segmental duplications in the genome.

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Filter fasta/fastq(.gz) files by ID and/or sequence length

Toolkit for processing sequences in FASTA/Q formats

Tools for population genetics on sequencing datas

SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.

Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.

sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.

SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.

SLR is a program to detect sites in coding DNA that are unusually conserved and/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree.

SMALT aligns DNA sequencing reads with a reference genome.

Reads from a wide range of sequencing platforms can be processed, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads are supported. There is no support for SOLiD reads.

SMRT Link is the web-based end-to-end workflow manager for the Sequel™ System. (installed in mode command line on our cluster)

Inference of ploidy and heterozygosity structure using whole genome sequencing data. This tool extracts heterozygous kmer pairs from kmer dump files (from jellyfish or KMC) and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Smudgeplots are computed from raw/trimmed reads and show the haplotype structure using heterozygous kmer pairs.

Gene prediction tool

SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

Rapid haploid variant calling and core genome alignment. Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree).

A fast and efficient program for estimating individual admixture coefficients based on sparse non-negative matrix factorization and population genetics.

SPAdes ﾖ St. Petersburg genome assembler ﾖ is intended for both standard isolates and single-cell MDA bacteria assemblies.

A collection of Phylogenetics tools for creating and manipulating networks and trees.

A C library that is bundled with much of the above software. C function library for sequence analysis.

Toolkit to query Short Reads Archive at NCBI

SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS  paired-read data.

SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads).

The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data. It does not need a pre-defined population model and can be applied to hundreds of unphased sequences.

RNA-seq aligner

STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set (using a GTF file, ideally the same annotation file used during the STAR genome index building process during the intial STAR setup).

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.

The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

Fast and exact clustering of sequences.

Sumatra was developed by the LECA and aims to compute a great deal of sequence similarities in a fast and exact way, based on the length of the Longest Common Subsequence (LCS) between two sequences. Sequence clustering based on similarities is also available through Sumaclust.

Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.

SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.

Structural variation and indel detection by local assembly

A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.

SVIM is a structural variant caller for long reads. It is able to detect, classify and genotype five different classes of structural variants.

Bayesian genotyper for structural variants.

TAB-delimited file IndeXer. Useful for vcfTools.

Tapestry is a tool to validate and edit small eukaryotic genome assemblies using long sequence reads. It is designed to help identify complete chromosomes, symbionts, haplotypes, complex features and errors in close-to-complete genome assemblies.

Trait Analysis by aSSociation, Evolution and Linkage. TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization for large sets of data.

Tigmint identifies and corrects misassemblies using linked reads from 10x Genomics Chromium.

Prediction of transmembrane helices in proteins.

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.

treePL is a phylogenetic penalized likelihood program.

TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees.

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Search for tRNA genes in genomic sequence.

Structural variant comparison tool for VCFs

Tools for handling Unique Molecular Identifiers in NGS data sets

VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.

An awk-like VCF parser