Cookbook index
List of gene tree workflows¶
In [1]:
!ete3 build workflows genetree
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GeneTree Workflows
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Worflow name | Description | threads
============================================= | ============================================================ | ==========
phylomedb4 | Worflow described in Huerta-Cepas, et al (Nucleic Acid Resea | 1
| rch, 2013) and used in http://PhylomeDB.org |
--------------------------------------------- | ------------------------------------------------------------ | ----------
eggnog41 | Workflow used in the EggNOG orthology database and based on | 1
| the phylomedb4 workflow |
--------------------------------------------- | ------------------------------------------------------------ | ----------
ensembl_small | Experimental (do not use yet) | 1
--------------------------------------------- | ------------------------------------------------------------ | ----------
ensembl_large | Experimental (do not use yet) | 1
--------------------------------------------- | ------------------------------------------------------------ | ----------
full_modeltest | Complete (and slow) pipeline testing all evolutionary models | 1
| and inferring tree with Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
full_modeltest_bootstrap | Complete (and slow) pipeline testing all evolutionary models | 1
| and inferring tree with Phyml and 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
full_fast_modeltest | Test all evolutionary models using NJ inference and computes | 1
| final tree with Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
full_fast_modeltest_bootstrap | Test all evolutionary models using NJ inference and computes | 1
| final tree with Phyml and 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
full_ultrafast_modeltest | Test all evolutionary models using NJ inference with no F, I | 1
| and G estimation and computes final tree with Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
full_ultrafast_modeltest_bootstrap | Test all evolutionary models using NJ inference with no F, I | 1
| and G estimation and computes final tree with Phyml and 100 |
| bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
soft_modeltest | Complete (and slow) pipeline testing 5 protein evolutionary | 1
| models and inferring tree with Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
soft_modeltest_bootstrap | Complete (and slow) pipeline testing 5 protein evolutionary | 1
| models and inferring tree with Phyml and 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
soft_fast_modeltest | Test 5 protein evolutionary models using NJ inference and co | 1
| mputes final tree with Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
soft_fast_modeltest_bootstrap | Test 5 protein evolutionary models using NJ inference and co | 1
| mputes final tree with Phyml and 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
soft_ultrafast_modeltest | Test 5 protein evolutionary models using NJ inference with n | 1
| o F, I and G estimation and computes final tree with Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
soft_ultrafast_modeltest_bootstrap | Test 5 protein evolutionary models using NJ inference with n | 1
| o F, I and G estimation and computes final tree with Phyml a |
| nd 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_raxml | Computes a tree using ClustalOmega with default parameters a | 1
| s aligner and RAxML |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_raxml_bootstrap | Computes a tree using ClustalOmega with default parameters a | 1
| s alignerand RAxML with 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_phyml | Computes a tree using ClustalOmega with default parameters a | 1
| s aligner and Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_phyml_bootstrap | Computes a tree using ClustalOmega with default parameters a | 1
| s aligner and Phyml and 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_fasttree | Computes a tree using ClustalOmega with default parameters a | 1
| s aligner and FastTree |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_trimmed_raxml | Computes a tree using default ClustalOmega as aligner, trimA | 1
| l for alg. cleaning and RAxML |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_trimmed_raxml_bootstrap | Computes a tree using ClustalOmega with default parameters, | 1
| trimAl for alg. cleaning and RAxML with 100 bootstraps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_trimmed_phyml | Computes a tree using ClustalOmega with default parameters, | 1
| trimAl for alg. cleaning as aligner and Phyml |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_trimmed_phyml_bootstrap | Computes a tree using ClustalOmega with default parameters, | 1
| trimAl for alg. cleaning as aligner and Phyml and 100 bootst |
| raps |
--------------------------------------------- | ------------------------------------------------------------ | ----------
standard_trimmed_fasttree | Computes a tree using ClustalOmega with default parameters, | 1
| trimAl for alg. cleaning as aligner and FastTree |
============================================= | ============================================================ | ==========
List of aligners¶
In [2]:
!ete3 build apps aligners
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aligners
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name | app type | desc.
==================== | ========== | ======================================================================
metaligner_phylomedb | metaligner | Meta-aligning based on head/tail alignments produced by muscle, mafft
| | and dialign-tx, scanned with M-Coffee. Unconsistent columns are remove
| | d and final alignment is cleaned with trimAl
-------------------- | ---------- | ----------------------------------------------------------------------
metaligner_trimmed | metaligner | Meta-aligning based on head/tail alignments produced by muscle, mafft
| | and clustalomega, scanned with M-Coffee. Unconsistent columns are remo
| | ved and final alignment is cleaned with trimAl
-------------------- | ---------- | ----------------------------------------------------------------------
metaligner_default | metaligner | Meta-aligning based on head/tail alignments produced by muscle, mafft
| | and clustalomega, scanned with M-Coffee. Unconsistent columns are remo
| | ved
-------------------- | ---------- | ----------------------------------------------------------------------
tcoffee_default | tcoffee | (EXPERIMENTAL) tcoffee alignment with default paramerters
-------------------- | ---------- | ----------------------------------------------------------------------
mcoffee_ensembl | tcoffee | (EXPERIMENTAL) mcoffee alignment as used in the Ensembl database
-------------------- | ---------- | ----------------------------------------------------------------------
muscle_default | muscle | muscle alignment with default parameters
-------------------- | ---------- | ----------------------------------------------------------------------
mafft_default | mafft | mafft alignment with default parameters
-------------------- | ---------- | ----------------------------------------------------------------------
mafft_einsi | mafft | mafft alignment using the E-INS-i mode
-------------------- | ---------- | ----------------------------------------------------------------------
mafft_linsi | mafft | mafft alignment using the L-INS-i mode
-------------------- | ---------- | ----------------------------------------------------------------------
mafft_ginsi | mafft | mafft alignment using the G-INS-i mode
-------------------- | ---------- | ----------------------------------------------------------------------
clustalo_default | clustalo | clustalo with default parameters
==================== | ========== | ======================================================================
List of aligner cleaners¶
In [3]:
!ete3 build apps "alg cleaners"
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alg cleaners
--------------------------------------------------------------------------------------
name | app type | desc.
=============== | ======== | =========================================================
trimal001 | trimal | trimal alignment cleaning removing columns with >1% gaps
--------------- | -------- | ---------------------------------------------------------
trimal01 | trimal | trimal alignment cleaning removing columns with >10% gaps
--------------- | -------- | ---------------------------------------------------------
trimal02 | trimal | trimal alignment cleaning removing columns with >20% gaps
--------------- | -------- | ---------------------------------------------------------
trimal03 | trimal | trimal alignment cleaning removing columns with >30% gaps
--------------- | -------- | ---------------------------------------------------------
trimal05 | trimal | trimal alignment cleaning removing columns with >50% gaps
--------------- | -------- | ---------------------------------------------------------
trimal_gappyout | trimal | trimal alignment cleaning using gappyout algorithm
=============== | ======== | =========================================================
List of model testers¶
In [4]:
!ete3 build apps "model testers"
---------------------------------------------------------------------------------------------------------------
model testers
---------------------------------------------------------------------------------------------------------------
name | app type | desc.
========================= | ========== | ======================================================================
prottest_default | prottest | Uses BioNJ trees to select best protein model from: JTT, WAG, VT, LG a
| | nd MtREV. Fixed parameters: +G+I+F
------------------------- | ---------- | ----------------------------------------------------------------------
pmodeltest_full_ultrafast | pmodeltest | Test all models using NJ tree inference and skipping gamma, invariant
| | sites, and frequency site estimations (!G!I!F)
------------------------- | ---------- | ----------------------------------------------------------------------
pmodeltest_full_fast | pmodeltest | Test all models using NJ tree inference
------------------------- | ---------- | ----------------------------------------------------------------------
pmodeltest_full_slow | pmodeltest | Test all models using ML tree inference
------------------------- | ---------- | ----------------------------------------------------------------------
pmodeltest_soft_ultrafast | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using NJ tree inference and skipping g
| | amma, invariant sites, and frequency site estimation (!G!I!F)
------------------------- | ---------- | ----------------------------------------------------------------------
pmodeltest_soft_fast | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using NJ tree inference
------------------------- | ---------- | ----------------------------------------------------------------------
pmodeltest_soft_slow | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using ML tree inference
========================= | ========== | ======================================================================
List of tree builders¶
In [5]:
!ete3 build apps "tree builders"
-----------------------------------------------------------------------------------------------------------
tree builders
-----------------------------------------------------------------------------------------------------------
name | app type | desc.
======================= | ======== | ======================================================================
bionj_default | phyml | BioNJ tree inferred with Phyml. default models JTT/GTR
----------------------- | -------- | ----------------------------------------------------------------------
fasttree_default | fasttree | Fasttree with default parameters
----------------------- | -------- | ----------------------------------------------------------------------
fasttree_full | fasttree | Fasttree with slow NNI and MLACC=3
----------------------- | -------- | ----------------------------------------------------------------------
phyml_default | phyml | Phyml tree using +G+I+F, 4 classes and aLRT branch supports. Default m
| | odels JTT/GTR
----------------------- | -------- | ----------------------------------------------------------------------
phyml_default_bootstrap | phyml | Phyml tree using +G+I+F, 4 classes and 100 bootstraps. Default models
| | JTT/GTR
----------------------- | -------- | ----------------------------------------------------------------------
raxml_default | raxml | RAxML with default parameters, GAMMA JTT/GTR and aLRT branch supports.
----------------------- | -------- | ----------------------------------------------------------------------
raxml_default_bootstrap | raxml | RAxML with default parameters, GAMMA JTT/GTR and 100 boostrap replicat
| | es
----------------------- | -------- | ----------------------------------------------------------------------
treebest_ensembl | phyml | (EXPERIMENTAL)
======================= | ======== | ======================================================================
List of species tree workflows¶
In [6]:
!ete3 build workflows supermatrix
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Supermatrix Workflows
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Worflow name | Description | threads
============================================= | ============================================================ | ==========
sptree_fasttree_100 | Selects COGs present in all target species, make a concatena | 1
| ted alignment and build a tree with FastTree |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_fasttree_95 | Selects COGs present in at least 95% of the target species, | 1
| make a concatenated alignment and build a tree with FastTree |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_fasttree_90 | Selects COGs present in at least 90% of the target species, | 1
| make a concatenated alignment and build a tree with FastTree |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_fasttree_85 | Selects COGs present in at least 85% of the target species, | 1
| make a concatenated alignment and build a tree with FastTree |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_fasttree_all | Selects all COGS regardless of how many species are represen | 1
| ted, make a concatenated alignment and build a tree with Fas |
| tTree |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_raxml_100 | Selects COGs present in all target species, make a concatena | 1
| ted alignment and build a tree with RAxML |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_raxml_95 | Selects COGs present in at least 95% of the target species, | 1
| make a concatenated alignment and build a tree with RAxML |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_raxml_90 | Selects COGs present in at least 90% of the target species, | 1
| make a concatenated alignment and build a tree with RAxML |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_raxml_85 | Selects COGs present in at least 85% of the target species, | 1
| make a concatenated alignment and build a tree with RAxML |
--------------------------------------------- | ------------------------------------------------------------ | ----------
sptree_raxml_all | Selects all COGS regardless of how many species are represen | 1
| ted, make a concatenated alignment and build a tree with RAx |
| ML |
============================================= | ============================================================ | ==========
Inspect workflow details¶
(ete3 build show for inspecting / ete3 build dump for raw ouput )
In [7]:
!ete3 build show standard_raxml
[genetree_meta_workflow] standard_raxml = clustalo_default-none-none-raxml_default [clustalo_default-none-none-raxml_default] _aa_tree_builder = @raxml_default _aa_aligner = @clustalo_default _nt_alg_cleaner = none _aa_model_tester = none _nt_tree_builder = @raxml_default _app = genetree _nt_aligner = @clustalo_default _aa_alg_cleaner = none _nt_model_tester = none _appset = @builtin_apps [clustalo_default] _desc = clustalo with default parameters _app = clustalo [raxml_default] _desc = RAxML with default parameters, GAMMA JTT/GTR and aLRT branch supports. _app = raxml _bootstrap = alrt _method = GAMMA _aa_model = JTT _model_suffix = -f = d -p = 31416
Inspect application details¶
(ete3 build show for inspecting / ete3 build dump for raw ouput )
In [8]:
!ete3 build show pmodeltest_soft_ultrafast
[pmodeltest_soft_ultrafast] _desc = Test JTT,WAG,VT,LG,MtREV models using NJ tree inference and skipping gamma, invariant sites, and frequency site estimation (!G!I!F) _app = pmodeltest _aa_models = JTT,WAG,VT,LG,MtREV _nt_models = GTR --fast = --noinv = --nogam =