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A new way to render phylogenetic data

🌳 Welcome to the iPhyloGeo++ wiki! 🌳

iPhyloGeo++ is a bioinformatics pipeline dedicated to the analysis of phylogeography. iPhyloGeo++ is an open-source multi-platform application designed by the team of Professor Nadia Tahiri (University of Sherbrooke, Quebec, Canada). It is implemented in Python. This tool can be used to obtain trees from climatic data of the regions where the samples have been collected. Those climatic trees are then used for topological and evolutionary comparison against phylogenetic trees from multiple sequence alignments (MSAs) using the Least Square (LS) metric. MSAs that yield trees with a significant LS value are then optionnally saved in folders with their respective tree. The output.csv file contains the informations of all the significant MSAs informations (see Worflow Section for more details).

aPhyloGeo++ offers the following features:

• Select a sequence Fasta file and climatic file in an accepted format (csv)
• Runs a global sequence alignment from the Fasta file.
• Shows climatic data with location
• Calculates the evolutionary distance depending on the topology with the climate provided using LS metric.
• Displays the MSAs that yield trees with a significant LS, it can be saved as csv.

References

First calculation of distance between phylogenetic tree : Least Square metric

Cavalli-Sforza, L. L., & Edwards, A. W. (1967). Phylogenetic analysis. Models and estimation procedures. American journal of human genetics, 19(3 Pt 1), 233.

Felsenstein, J. (1997). An alternating least squares approach to inferring phylogenies from pairwise distances. Systematic biology, 46(1), 101-111.

Makarenkov, V., & Lapointe, F. J. (2004). A weighted least-squares approach for inferring phylogenies from incomplete distance matrices. Bioinformatics, 20(13), 2113-2121.

Second calculation of distance between phylogenetic tree : Robinson-Foulds metric

Robinson, D.F. and Foulds, L.R., 1981. Comparison of phylogenetic trees. Mathematical biosciences, 53(1-2), pp.131-147.

Full dataset description : Analysis of genetic and climatic data of SARS-CoV-2

Koshkarov, A., Li, W., Luu, M. L., & Tahiri, N. (2022). Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2.

Contact 📧

Please email us at : [email protected] for any question or feedback.