extending the iplant de: a phylogenetics workflow
TRANSCRIPT
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