Get Started on TriFusion


Installers are available for Windows, MacOS and several Unix distro's. PPAs are available Debian and Ubuntu and AUR packages for ArchLinux.

User Guide

Get the lattest documentation on the full features of TriFusion, how to operate GUI and command line versions of TriFusion, and more!

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View on GitHub

TriFusion is and will always be free software (under GPLv3 license). Feel free to view and modify the source code, hosted on GitHub.

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Handling phylogenomic data is much easier now.

TriFusion was specifically developed to streamline several stages of phylogenomic and population genomic projects, from the gathering of orthologs from hundreds of proteomes, to the processing of thousands of alignment files, to data exploration via an assortment of graphical and statistical analyses.

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Gather and explore orthologs from multiple proteomes with just a few clicks.

Load proteome files in Fasta format from hundreds of species into TriFusion and get the full coverage of high quality ortholog clusters with minimal user input. Take advantage of several filters and graphical options to explore your ortholog groups and export them into protein and/or nucleotide sequences.

See Orthology features
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Convert, concatenate, filter, collapse alignments and so much more!

TriFusion offers a wide variety of useful and common operations that can be quickly and easily applied to thousands of alignment files. Want to collapse identical sequences into haplotypes? Check! Want to filter alignments with excess of missing data? Check! Want to remove certain codon positions? Check! Want to create a consensus from multiple sequences in an alignments? Check! See the user manual for the complete set of operations that you can do.

See Process features
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Full graphical visualization of your data

TriFusion tackles one of the biggest challenges in big phylogenomic and population genomics projects: How to explore your data quickly and efficiently. Designed from the start to handle thousands of alignment files, the Statistics module offers dozens of statistical and graphical options to explore your data according to four main categories: General Information, Polymorphism and Variation, Missing Data and Outlier Dectection

See Statistics features
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For command line lovers <3

Almost all functionalities of TriFusion can be executed from a terminal by using the appropriate CLI programs: orthomcl_pipeline (Orthology Search), TriSeq (Process) and TriStats (Statistics). The CLI programs are faster, modular and can be easily included in your scripts. This also means that TriFusion can be executed in "GUI-free" servers for tasks that may require high uptimes and/or computational resources.

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Jump right in into TriFusion using any of the following quick start guides. These are sorted according to TriFusion's three main modules: