Joshua-Levy-Synteny-Analysis

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:

Note: Delete Sort Files after every analysis

Using SyntenyFinal.py and Circos.py:

1. 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

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

Using findGhostSegments:

Using CNS Analysis (workwithMAF and manipulateFilesTest):

What to do after CNS Analysis Completes:

1. Convert fasta files to phylip files and run them under PhyML to generate trees. Can visualize these trees using FigTree.
2. If using NERSC, module load PhyML. ^^^