Bases: ete2.phylo.phylotree.PhyloNode
Re-implementation of the standart TreeNode instance. It adds attributes and methods to work with phylogentic trees.
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change dist/branch length of the tree to a given evolutionary variable (dN, dS, w or bL), default is bL.
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returns node list corresponding to a given idname
returns one precomputed model
Parameters: | modelname – string of the name of a model object stored |
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Returns: | Model object |
Returns pvalue of LRT between alternative model and null model.
usual comparison are:
Alternative | Null | Test |
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M2 | M1 | PS on sites (M2 prone to miss some sites) (Yang 2000) |
M3 | M0 | test of variability among sites |
M8 | M7 | PS on sites (Yang 2000) |
M8 | M8a | RX on sites?? think so.... |
bsA | bsA1 | PS on sites on specific branch (Zhang 2005) |
bsA | M1 | RX on sites on specific branch (Zhang 2005) |
bsC | M1 | different omegas on clades branches sites ref: Yang Nielsen 2002 |
bsD | M3 | different omegas on clades branches sites (Yang Nielsen 2002, Bielawski 2004) |
b_free | b_neut |
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b_free | M0 | different ratio on branches (Yang Nielsen 2002) |
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same function as for phyloTree, but translate sequences if nucleotides nucleotidic sequence is kept under node.nt_sequence
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function to mark branches on tree in order that paml could interpret it. takes a “marks” argument that should be a list of #1,#1,#2 e.g.:
t=Tree.mark_tree([2,3], marks=["#1","#2"])
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call super show adding up and down faces
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To compute evolutionnary models. e.g.: b_free_lala.vs.lele, will launch one free branch model, and store it in “WORK_DIR/b_free_lala.vs.lele” directory
WARNING: this functionality needs to create a working directory in “rep”
WARNING: you need to have codeml and/or SLR in your path
The models available are:
Model name | Description | Model kind |
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M1 | relaxation | site |
M10 | beta and gamma + 1 | site |
M11 | beta and normal > 1 | site |
M12 | 0 and 2 normal > 2 | site |
M13 | 3 normal > 0 | site |
M2 | positive-selection | site |
M3 | discrete | site |
M4 | frequencies | site |
M5 | gamma | site |
M6 | 2 gamma | site |
M7 | relaxation | site |
M8 | positive-selection | site |
M8a | relaxation | site |
M9 | beta and gamma | site |
SLR | positive/negative selection | site |
M0 | negative-selection | null |
fb_anc | free-ratios | branch_ancestor |
bsA | positive-selection | branch-site |
bsA1 | relaxation | branch-site |
bsB | positive-selection | branch-site |
bsC | different-ratios | branch-site |
bsD | different-ratios | branch-site |
b_free | positive-selection | branch |
b_neut | relaxation | branch |
fb | free-ratios | branch |
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call super show of PhyloTree histface should be a list of models to be displayes as histfaces
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Inherits from Tree but adds the tenth format, that allows to display marks for CodeML. TODO: internal writting format need to be something like 0
Returns the newick representation of current node. Several arguments control the way in which extra data is shown for every node:
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Example:
t.get_newick(features=["species","name"], format=1)
alias of EvolNode