Purdue University

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.

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.

Svtools is a suite of utilities designed to help bioinformaticians construct and explore cohort-level structural variation calls.

SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data. svtyper is the original implementation of the genotyping algorithm, and works with multiple samples.

swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties.

SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ header files and using them to generate the wrapper code that scripting languages need to access the underlying C/C++ code. In addition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit your application.

Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.

T-coffee is a multiple sequence alignment software using a progressive approach.

Talon is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets.

TargetP-2.0 tool predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (luTP). For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.

TASSEL is a software package used to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.

Taxonkit is a practical and efficient NCBI taxonomy toolkit.

Tcl Tool Command Language is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Open source and business-friendly, Tcl is a mature yet evolving language that is truly cross platform, easily deployed and highly extensible.

Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors.

Tecplot 360 is a Computational Fluid Dynamics (CFD) and numerical simulation software package used in post-processing simulation results. It is also used in chemistry applications to visualize molecule structure by post-processing charge density data.

TensorFlow is an end-to-end open source platform for machine learning.

Tetranscripts is a package for including transposable elements in differential enrichment analysis of sequencing datasets.

TeX Live is a free software distribution for the TeX typesetting system. Heads up, its is not a reproducible installation. At any point only the most recent version can be installed. Older versions are included for backward compatibility, i.e., if you have that version already installed.

Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallman and Bob Chassell many years ago, loosely based on Brian Reids Scribe and other formatting languages of the time. It is used by many non-GNU projects as well.

TFlearn is a modular and transparent deep learning library built on top of Tensorflow. It was designed to provide a higher-level API to TensorFlow in order to facilitate and speed-up experimentations, while remaining fully transparent and compatible with it.