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Thank you for choosing getphylo and welcome to the wiki!
Here you can find information on installation and basic usage as well as some more advanced use cases. There is also a full list and description of the parameters getphylo uses.
getphylo is a tool for building phylogentic trees from genbank files. It uses heuristic methods to quickly identify singletons (protein coding sequences that have no paralogues) in the provided genbank files, aligns them and builds a tree from the combined alignments. For example, if your genbank files contain whole genomes, getphylo will construct a multi-locus phylogenomic tree. However, genbank files could contain other genetic elements such as chromosomes, plasmids or gene clusters.
getphylo's de novo approach means that it is not limited in its taxonomic scope. The same method can be applied equally to bacteria, archaea or eukaryotic genomes. This makes it a powerful and flexible tool.
For more information on getphylo's design and theoretical implications, please read the paper - see below.
If you use getphylo, please cite:
Booth, T. J., Shaw, S., & Weber, T. (2023). getphylo: rapid and automatic generation of multi-locus phylogenetic trees. BioRxiv, 2023.07.26.550493.