Software

Freely available software for computational biology developed by UF researchers.

This page lists downloadable software programs. Web-based tools are described in a separate page.

BioSpique

Binding site detection with spiking neural networks.

BISSCA

BISulfite Sequencing Comparative Analysis.

cscall

Genome-wide methylation analysis.

Demux

Managing barcodes in FASTA or FASTQ files.

FASTools

Utilities for large FASTA or FASTQ files.

dibig_tools

Utilities for HiPerGator.

KBAS

Association studies for complex diseases.

MethylMapper

Tools for high-throughput methylation analysis

NPACT

Gene idendification and sequence annotation.

PANGEA

Pipeline Analysis for Next GEneration Amplicons.

PASTA

Alternative splicing analysis with RNA-Seq – junction identification.

PASTA2

Alternative splicing analysis with RNA-Seq – isoform reconstruction.

pymapper

Python client for the MAPPER database of predicted transcription factor binding sites.

TaxCollector

Tools for the RDP 16S RNA database.