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Index

1.fasta
Loading and using Sankoff | Loading and using Sankoff
3.fasta
Loading a Direct Optimization
35.san
Loading and using Sankoff | Loading and using Sankoff
5.fasta
Loading a Direct Optimization
bootstrap
Calculating Supports: Jackknife
build
Loading and using Sankoff | Loading a Direct Optimization | Executing scripts
calculate_support
Calculating Supports: Jackknife | Calculating Supports: Jackknife
calculate_support (jackknife)
Calculating Supports: Jackknife
calculate_supports (bremer)
Calculating Supports: Bremer
cd
Loading and using Sankoff | Loading and using Sankoff | Loading and using Sankoff | Loading and using Sankoff | Loading and using Sankoff
constraint
Trees argument
constraint.txt
Trees argument
course.fasta:0
Modifying your characters with
cross_references
Loading a Direct Optimization
data
Modifying your characters with
exit
Loading and using Sankoff
fuse
Tree Fusing | Tree Fusing | Tree Fusing | Tree Fusing
fuse ()
Tree Fusing
gap_opening
Modifying your characters with
help ()
Using the Interactive Console | Using the Interactive Console
ia
Modifying your characters with
implied_alignment
Modifying your characters with
perturb
Perturbing trees for improved | Perturbing trees for improved | Perturbing trees for improved | Perturbing trees for improved
perturb ()
Perturbing trees for improved
pwd
Loading and using Sankoff
ratchet
Perturbing trees for improved
read
Loading and using Sankoff | Loading and using Sankoff | Loading and using Sankoff | Loading and using Sankoff | Loading and using Non-additive | Searching the local neighborhood
read (*.fasta)
Loading and using Sankoff
recover
Trees argument
report
Loading and using Sankoff | Loading a Direct Optimization | Loading a Direct Optimization | Searching the local neighborhood
report (data)
Using the Interactive Console | Using the Interactive Console
report (diagnosis)
Using the Interactive Console | Using the Interactive Console
report (treestats)
Using the Interactive Console
search
Using Search | Using Search
select
Loading and using Sankoff
store ()
Searching the local neighborhood
store (name)
Searching the local neighborhood
swap
Searching the local neighborhood | Searching the local neighborhood | Trees argument | Trees argument | Executing scripts | Tree Fusing | Tree Fusing | Tree Fusing | Tree Fusing
swap ()
Searching the local neighborhood
tbr_trees.tree
Trees argument
tcm:(1,1)
Modifying your characters with
tcm:(1,2)
Modifying your characters with
tcm:(2,1)
Modifying your characters with | Modifying your characters with
threshold
Trees argument
timeout
Trees argument
trajectory
Trees argument
transform
Loading and using Sankoff | Modifying your characters with | Modifying your characters with | Perturbing trees for improved
transform (static_approx)
Modifying your characters with
trees
Trees argument
use ()
Searching the local neighborhood
use (name)
Searching the local neighborhood
visited
Trees argument | Trees argument | Calculating Supports: Bremer
visited_trees.txt
Trees argument
weight
Modifying your characters with
wipe
Searching the local neighborhood
wipe ()
Searching the local neighborhood



Andres Varon, avaron@amnh.org