modify phase1 and phase2 to follow structure of generating gene trees then sequences instead

[August Guang]

phase1 and phase2 should be redone more intuitively, so that we instead have 2 python scripts of genetrees.py and genesequences.py, where one generates gene trees given a species tree and the other generates gene sequences given a gene tree.

[August Guang]

resolved in commit 488dfa2