Y Software

Software for applications of SNPs on the Y chromosome: button for snptotree button for phyloimpute

SNPtotree

SNPtotree identifies which biallelic variants on non-recombining DNA have phylogenetic properties based on sequencing data and establishes a phylogenetic tree of these variants.

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Installation and Getting Started

Command-line tool is available on github including installation and getting started documentation:

You can also follow this step-by-step tutorial:

Communication

Peer-reviewed publication: Köksal, Z.; Børsting, C.; Gusmão, L.; Pereira, V. SNPtotree—Resolving the Phylogeny of SNPs on Non-Recombining DNA. Genes 2023, 14, 1837. https://doi.org/10.3390/genes14101837

Oral presentation at ISMB/ECCB 2023:

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Poster presentation at 8th Annual Danish Bioinformatics Conference 2024:

Case Study

Generating phylogenetic tree of Native American haplogroup Q (Aug 2024): Application of Targeted Y-Chromosomal Capture Enrichment to Increase the Resolution of Native American Haplogroup Q

PhyloImpute

PhyloImpute imputes missing SNP data on haploid DNA by leveraging the SNPs’ phylogeny in a selected phylogenetic tree. The user can further explore the data and its quality. This includes a haplogroup prediction that is highly customizable using a preinstalled or custom phylogenetic tree. The user can identify sample mixtures, backmutations and recurrent mutations. Finally, sequencing errors and erroneous/incomplete tree structures can be identified.

Description of GIF

Installation and Getting Started

Command-line tool is available on github including installation and getting started documentation:

The software is also available with a graphical user interface for Windows:
Download the compressed folder by clicking on the button, unzip the folder, access folders PhyloImpute1_Windows, dist, and phyloimpute_windows. Double-click the phyloimpute_windows.exe file and navigate through the graphical user interface.

Communication