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Index

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

American Museum of Natural History

Central Park West at 79th Street
New York, NY 10024-5192
Phone: 212-769-5100

Open daily from 10 am - 5:45 pm
except on Thanksgiving and Christmas
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