Purdue University

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Theano is most commonly used to perform Deep Learning and has excellent GPU support and integration through PyCUDA.

Thermo-Calc allows you to calculate the state for a given thermodynamic system to obtain insight.

Tiara is a deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.

Tigmint identifies and corrects misassemblies using linked (e.g. MGI's stLFR, 10x Genomics Chromium) or long (e.g. Oxford Nanopore Technologies long reads) DNA sequencing reads.

Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more.

Tobias is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.

Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. Tombo also provides tools for the analysis and visualization of raw nanopore signal.

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

TorchANI is a PyTorch-based program for training/inference of ANI (ANAKIN-ME) deep learning models to obtain potential energy surfaces and other physical properties of molecular systems.

TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables.

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

Transabyss is a tool for De novo assembly of RNAseq data using ABySS.

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

Transrate is software for de-novo transcriptome assembly quality analysis.

Transvar is a multi-way annotator for genetic elements and genetic variations.

tRAX (tRNA Analysis of eXpression) is a software package built for in-depth analyses of tRNA-derived small RNAs (tDRs), mature tRNAs, and inference of RNA modifications from high-throughput small RNA sequencing data.

Treetime is a tool for maximum likelihood dating and ancestral sequence inference.

Trim-galore is a wrapper tool that automates quality and adapter trimming to FastQ files.

Trimal is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.

Trimmomatic is a flexible read trimming tool for Illumina NGS data.