#5 MLST based core phylogeny

[jacastillo]

I wonder how we can perform MLST based core phylogeny in BPGA. It says ‘refer tutorial’ but there’s no tutorial and User Manual instructions are insufficient.

[Narendrakumar Chaudhari]

For MLST analysis, BPGA will halt and allow the user to make required changes.
For MLST analysis, on user defined housekeeping genes Check "mlst_core.txt"
for gene details and copy the respective cluster IDs from the first column to
"CORE_MLST.txt".
CORE_MLST file has core gene family IDs , If you keep only desired IDs phylogeny will run on only those present in CORE_MLST file. You can select by looking at the gene names in mlst_core.txt file. and copy only desired IDs from mlst_core.txt to CORE_MLST file.
Both the files are present in Bin folder of BPGA Executables. Save and close the files before proceeding further.
If you Press enter after the MLST notice is shown, then BPGA will continue without this step, 20 random cluster IDs will be used for core phylogeny.