Extract single copy marker genes


Phylogenetic markers are genes (and proteins), which can be used to reconstruct the evolutionary history of different organisms. One classical phylogenetic marker is the 16S ribosomal RNA gene, which is often-used, but also known to be a sub-optimal phylogenetic marker for some organisms. Efforts to find a suitable set of protein coding phylogenetic marker genes [1, 2] led to the identification of 40 universal single copy marker genes (MGs). These 40 marker genes occur in single copy in the vast majority of known organisms and they were used to successfully reconstruct a phylogenetic tree of life [1].

The tool fetchMGs extracts the 40 MGs from genomes and metagenomes in an easy and accurate manner. This is done by utilizing Hidden Markov Models (HMMs) trained on protein alignments of known members of the 40 MGs as well as calibrated cutoffs for each of the 40 MGs. Please note that these cutoffs are only accurate when using complete protein sequences as input files. The output of the program are the protein sequences of the identified proteins, as well as their nucleotide sequences, if the nucleotide sequences of all complete genes are provided as an additional input.

The most current version (v1.1) of fetchMGs can be downloaded from GitHub.

The legacy version (v1.0) can be downloaded from here.