autoMLST is a webserver and analysis pipeline for constructing species phylogenies from genomic data. The pipeline scans for conserved single copy housekeeping genes, selects comparable genomes in the database, and builds a phylogeny using either a concatenated gene matrix or coalescent tree method.
This is not the official automlst repository, and is not currently maintained.
For full instructions and the official repository see autoMLST on bitbucket.
The simplified_wrapper.py script constructs an MLSA-based tree from a directory of Genbank files. Conserved single copy housekeeping genes are identified and a tree built from a concatenated gene matrix. However, no comparable genomes are added, nor are existing genomes removed.
Usage: simplified_wrapper.py directory
NOTE: reducedcore.zip needs to be unpacked before running.