extending the iplant de: a phylogenetics workflow
TRANSCRIPT
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Extending the iPlant DE: A Phylogenetics Workflow
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Infer the state of a continuous trait along a phylogeny
and estimate its rate of evolution.
Continuous Ancestral Trait Reconstruction
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Ancestral state of Hawaiian lobelioids
Lobelia niihauensis (Image: David Eickhoff)
Cyanea leptostegia (Image: Karl Magnacca)
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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)
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(Schulter et al. 1997, Paradis 2004)
Continuous Ancestral Character Estimation Ti
me
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Obtain sequences• GetSeq
Align sequences• Muscle
Build Tree
• Ninja (NJ)
Integrate Data
• Lopper
Run Analysis• CACE• DACE• Contrast• OUch• Picante• Penalized
likelihoodTraits
Seq IDs
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Obtain sequences• GetSeq
Align sequences• Muscle
Build Tree
• Ninja (NJ)Integrate
Data• Lopper
Run Analysis• CACETraits
Seq IDs
CACE Phylogenetic Workflow
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1. Select the Apps2. Order the Apps3. Map Outputs to Inputs4. Run the analysis
As Easy as 1-2-3-4
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Step 0
Become familiar with the Apps you are going to use:
inputs, outputs and options.
Modify as necessary.
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HANDS ON / DEMO
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Obtain sequences• GetSeq
Align sequences• Muscle
Build Tree
• Ninja (NJ)Integrate
Data• Lopper
Run Analysis• CACETraits
Seq IDs
CACE Phylogenetic Workflow
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Seq IDs
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Seq IDsTraits
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Seq IDsTraits
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