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Macro-synteny phylogeny

Before run the pipeline:

  1. install the lasest verion of SOI by python3 setup.py install, and have a check: which soi-syn;
  2. completed the example pipeline to get the orthologous synteny file collinearity.ortho;
  3. prepare file species.config to set the expected subgenome numbers for the targeted species (TAB seperated):
Vitis_vinifera  1
Aralia_elata    2
Centella_asiatica       2

Then run the pipeline:

cd phylogenomics
soi-syn anchor_trees collinearity.ortho species.config ../pep.faa ../all_species_gene.gff output_dir

After the pipeline completed, you can find tree files in the output_dir:

OG*treefile		# gene tree file for each anchor gene
chr*treefile	# macro-synteny tree file by concatenating the anchor genes from the same chromosome set
CHR*treefile	# macro-synteny tree file, but allowing gene missing

For example, CHR_Ae11-Ae15-Ca2-Ca7-Vv1_143_283.concat.treefile, Ae11-Ae15-Ca2-Ca7-Vv1 is the chromosome set, 143 is the number of anchor genes, and 283 is the number of all syntenic genes allowing missing.