Purdue University

Fastq_pair is used to match up paired end fastq files quickly and efficiently.

Fastspar is a tool for rapid and scalable correlation estimation for compositional data.

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.

FFTW is a C subroutine library for computing the discrete Fourier transform DFT in one or more dimensions, of arbitrary input size, and of both real and complex data as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST. We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

FFTW AMD Optimized version is a comprehensive collection of fast C routines for computing the Discrete Fourier Transform DFT and various special cases thereof.

A File Transfer Protocol client (FTP client) is a software utility that establishes a connection between a host computer and a remote server, typically an FTP server.

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

Flye: Fast and accurate de novo assembler for single molecule sequencing reads.

Fq is a command line utility for manipulating Illumina-generated FastQ files.

Fraggenescan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

FragGeneScanRs is a better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads. Its command line interface is backward compatible and adds extra features for more flexible usage. Compared to the original C implementation, shotgun metagenomic reads are processed up to 22 times faster using a single thread, with better scaling for multithreaded execution.

Freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.

Fseq is a feature density estimator for high-throughput sequence tags.

Funannotate is a genome prediction, annotation, and comparison software package.

Fwdpy11 is a Python package for forward-time population genetic simulation.

GADMA is a command-line tool. Basic pipeline presents a series of launches of the genetic algorithm followed by local search optimization and infers demographic history from the Allele Frequency Spectrum of multiple populations (up to three).