#Tutorial 1: Basic Search
read ("mol1.txt")
build (100)
select (unique)
swap (threshold:10)
select ()
report (asciitrees)
report ("tutorial1_trees.txt", trees)
report ("tutorial1_stats.txt", treestats)

#Tutorial2: Advanced Search I: Multiple Datasets and Data Types, Equal Weighting, rooting, and Publication Quality Trees
read ("mol2.txt", "morph.txt")
set (root: "Hagfish")
transform ((all, tcm:(1,1)))
select (unique)
build (100)
swap (threshold:10)
select ()
report (asciitrees)
report ("tutorial2", graphtrees)
report ("tutorial2_trees.txt", trees)
report ("tutorial2_stats.txt", treestats)

#Tutorial3: Advanced Search II: Tree Fusing and Frament Ratcheting
build (100)
select (unique)
fuse ()
select ()
perturb (iterations:10, ratchet:(0.2,5))
select ()
swap (threshold:10)
select ()
report ("tutorial3", graphtrees)
report ("alignment3.ss", phastwinclad)

#Tutorial4: Advanced Search III: Input Trees and Step Matrices
read ("trees.txt")
transform ((all, tcm:"g4ts1tv2.txt"), (static, weightfactor:4))
swap (threshold:10)
select ()
report ("tutorial5", graphtrees)

#Tutorial5: Support I: Bremer Support
transform ((all, tcm:(1,1)), (static, weightfactor:1))
swap ()
calculate_support (bremer, build (trees:5), swap (trees:2))
report (supports)

#Tutorial6: Support II: Bootstrap Support Using Dynamic Homology
calculate_support (bootstrap: 100, build(trees:2), swap(trees:1))
report (supports)

#Tutorial7: Support III: Bootstrap Support Using Static Homology
transform ((all, static_approx))
calculate_support (bootstrap: 100, build(trees:2), swap(trees:1))
report (supports)

#Tutorial8: Chromosome Analysis: Unnotated Sequences
wipe ()
read (chromosome:("mit5.txt"))
transform ((all, dynamic_pam:(inversion:15, indel:(10, 1.5), median:  3, swap_med:5, circular:true, approx:true)))
build (5)
swap ()
select ()
transform ((all, dynamic_pam:(inversion:15, indel:(10, 1.5), median:3, swap_med:5, circular:true, approx:false)))
swap ()
select ()
report (asciitrees)
report (trees)