Quick Marker Selection for Species Trees
You need to install: ete3 pandas
Steps:
- Create gene families of homologous sequences (you can use MCL or Silix, for instance)
- Select gene families that: ** Are represented in most species (a rule of thumb, use gene families that have more than 80% of your species) ** The number of sequences is similar to the number of species
- Compute gene trees for those gene families (using for instance IQ tree)
- Sequences should be named: nameOfSpecies_sequenceIdentifier
- Put all the resulting trees in the same folder
- Launch QMS:
python QMS.py folder_with_candidate_trees output_folder_name