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