###Integrated Analysis of Synteny (Multiple Synteny Comparison for Multiple Alignment, Circos Outputs, Allmaps Genome Reconstructions), Find Ghost Genes, Identify and Analyze CNS Elements from Multiple Alignment Files and More!
##Using Integrated Analysis: 1.
Note: Delete Sort Files after every analysis
###Using SyntenyFinal.py and Circos.py:
- See their relevant readmes
###Using AllMAPS: (Must run on linux or linux server, for now) Recommend: Run through the integrated analysis by setting performALLMAPS = 1 1.
###Using ALLMAPS_alternate: (Must run on linux or linux server, for now) Recommend: Run through the integrated analysis by setting performALLMAPSAlt = 1, must set performALLMAPS = 0 1.
##Using findGhostSegments: 1.
##Using CNS Analysis (workwithMAF and manipulateFilesTest): 1.
###What to do after CNS Analysis Completes:
- Convert fasta files to phylip files and run them under PhyML to generate trees. Can visualize these trees using FigTree.
- If using NERSC, module load PhyML. ^^^