Extending the iPlant DE: A Phylogenetics Workflow

Infer the state of a continuous trait along a phylogeny

and estimate its rate of evolution.

Continuous Ancestral Trait Reconstruction

Ancestral state of Hawaiian lobelioids

Lobelia niihauensis (Image: David Eickhoff)

Cyanea leptostegia (Image: Karl Magnacca)

Lobelia

_kauaensis

Lobelia

_villosa

Lobelia

_gloria-m

ontis

Tremato

lobelia_kauaiensis

Tremato

lobelia_macro

stach

ys

Lobelia

_hypoleuca

Lobelia

_yuccoides

Lobelia

_niihauensis

Brighamia_insig

nis

Brighamia_ro

ckii

Delisse

a_rhytidosp

erma

Delisse

a_subco

rdata

Cyanea_pilosa

Cyanea_acuminata

Cyanea_hirtella

Cyanea_coria

cea

Cyanea_leptoste

gia

Clermontia_kakeana

Clermontia_parviflora

Clermontia_arb

oresce

ns

Clermontia_faurie

i0

2

4

6

8

10

12

14

16

Maximum Height (m)

(Schulter et al. 1997, Paradis 2004)

Continuous Ancestral Character Estimation Ti

me

Obtain sequences• GetSeq

Align sequences• Muscle

Build Tree

• Ninja (NJ)

Integrate Data

• Lopper

Run Analysis• CACE• DACE• Contrast• OUch• Picante• Penalized

likelihoodTraits

Seq IDs

Obtain sequences• GetSeq

Align sequences• Muscle

Build Tree

• Ninja (NJ)Integrate

Data• Lopper

Run Analysis• CACETraits

Seq IDs

CACE Phylogenetic Workflow

1. Select the Apps2. Order the Apps3. Map Outputs to Inputs4. Run the analysis

As Easy as 1-2-3-4

Step 0

Become familiar with the Apps you are going to use:

inputs, outputs and options.

Modify as necessary.

HANDS ON / DEMO

Obtain sequences• GetSeq

Align sequences• Muscle

Build Tree

• Ninja (NJ)Integrate

Data• Lopper

Run Analysis• CACETraits

Seq IDs

CACE Phylogenetic Workflow

Seq IDs

Seq IDsTraits

Seq IDsTraits