Build phylogenomic tree

Build a phylogenomic tree of a set of bacterial or archaeal genomes based on multiple universal marker genes. Analysis includes gene extraction, multiple sequence alignment, model selection, tree construction and rooting. The client provides genome sequences.

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Our analysis starts with multiple genomes in fasta file format, and delivers a rooted phylogenomic tree whose tips (leafs) represent the input genomes. The analysis involves the following main steps:

• Detect and identify protein-coding genes in each genome.
• Determine and extract the "core" genes, i.e., shared by all genomes.
• Create a multiple sequence alignment for each core gene, and then concatenate those alignments.
• Select an optimal sequence evolution model and estimate a phylogeny based on the concatenated alignments, using IQtree.
• Estimate the placement of the tree's root.

In addition to the phylogeny, we also provide a thorough Materials & Methods writeup for use in your publications.

• At least 3 high-quality prokaryotic genomes, ideally from pure culture and at least 95% complete.
• Each genome must be stored in a distinct fasta file, and may consist of multiple contigs (the fewer the better).

	Prochlorococcus_tree_rooted.tre	Rooted phylogenomic tree of multiple Prochlorococcus genomes, in Newick file format.
	Concatenated_core_gene_alignments.fasta.gz	Concatenated alignments of all core genes, in fasta file format.

Main databases and software used in this analysis:

• Castor R package
• eggNOG
• diamond
• IQtree2
• HMMER
• MAFFT
• Prodigal

• Kapli, P., Yang, Z., Telford, M. J. (2020). Phylogenetic tree building in the genomic age. Nature Reviews Genetics 21:428-444
• Stott, C. M., Bobay, L. (2020). Impact of homologous recombination on core genome phylogenies. BMC Genomics 21:829

Price starts at $50 base + $10 per genome. Final price may differ depending on user settings, and will be available prior to order submission. Log in to see availability and payment modalities.