Package: trifusion
TriFusionMaking life easier for phylogenomic data gathering, processing and visualizationWebsite:http://odiogosilva.github.io/TriFusion/:loudspeaker: ANNOUNCING:TriFusion 1.0.0 is live!:tada: :balloon:What is TriFusion?TriFusion is a modern GUI and command line application designed to make the life of anyone withproteomeand/oralignment sequence dataeasier and more pleasurable. Regardless of your experience in bioinformatics, TriFusion is easy to use and offers a wide array of powerfull features to help you deal with your data. At the same time, it was developed to handle the enormous amount of data that is generated nowadays.TriFusion is an open source, cross-platform application written inPython 2.7and using theKivyframework to build the graphical interface.What can TriFusion do for you?Here is an overview of what it can do for you across its three main modules.Orthology - Search and explore orthologs across proteomesSearches for ortholog sequencesacross multiple species.Filters ortholog sequences according to thegene copy numberand/ornumber of taxapresent.Graphical visualizationof ortholog data.Exports your orthologs asprotein or nucleotide sequences.Find out moreProcess - Blazing fast processing of alignment filesConversionorconcatenationof alignment files into several popular formats (check supported formats).Collapseidentical sequences into the same haplotype.Createconsensussequences for each alignment with several options on how to handle sequence variation.Filtereither alignments (according to whether they contain or exclude certain taxa, to a minimum proportion of taxa, and/or variable sites) or alignment columns (according to codon position, missing data and gaps).Code indel patternsof your alignments into a binary matrix that is appended to the alignment.Revert concatenated alignmentsor export sub-regions into individual filesSetgene and codon partitionsas well assubstitution models(Nexus format)Createfile/taxa groupsto quickly perform operations on different sets of data.It'sfastandmemory efficient. Converting 3,093 files with 376 taxa can be performed in just 30 seconds and using less than 90Mb of RAM memory (check the benchmarks table).Find out moreStatistics - Effortless visual exploration of your dataProvides instant information on overall and per genesummary statistcs.TriFusion offersdozens of graphical and statistical optionsto explore your data:General information plots.Polymorphism and sequence variation plots.Missing data plots.Outlier plots.Publication ready figuresFind out moreInstallationExecutables binaries (GUI version only)The latest stable release of TriFusion can be installed as a standalone application using one of the following installers. Thisonly includes the GUI componentof TriFusion. If you also want the command line version, seeInstallation from source.LinuxDebian package based (See list):TriFusion-1.0.0rc1.debRPM package based (See list):TriFusion-1.0.0rc1.rpmArchLinux/Manjaro (See list):TriFusion-1.0.0.tar.xzis available on AUR.MacOSTriFusion-1.0.0rc1.app.zipWindowsTriFusion-1.0.0rc1 64bit installerTriFusion-1.0.0rc1 32bit installerNote for Windows 8.x and 10 users:Executing the TriFusion installer may generate a warning from SmartScreen. To continue with the installation, click the "More info" label and then "Run anyway".Installation from sourceTriFusion is onPyPiand can be easily installed withpip.# Install locally, without sudo permissions, using the --user flag
pip install trifusion --userNote that TriFusion is a python2 application, so make sure that yourpipis from the correct python version. If python3 is the default installation on your machine, you may need to runpip2instead.By itself, this command will only install the command line version of TriFusion. If you want to install the complete TriFusion package with the GUI libraries,follow these instructions according to your operating system.If you are unconvinced that a terminal version would be useful/pratical, check out how easy and fast it is to use TriFusion to process 614 Fasta alignments into phylip and nexus output formats :-):How to useTutorials on how to use TriFusion for its many tasks can be perusedhere.DocumentationYou can download TriFusion User Guidehere.CitationWhen using OrthoMCL to find ortholog clusters, please cite the original software:Fischer, S., Brunk, B. P., Chen, F., Gao, X., Harb, O. S., Iodice, J. B., Shanmugam, D., Roos, D. S. and Stoeckert, C. J. Using OrthoMCL to Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes Into New Ortholog Groups Current Protocols in Bioinformatics. 2011 35:6.12.1-6.12.19.We're working on a manuscript for TriFusion now.