EvolTree class

class EvolNode(newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x4063b18>, format=0, binpath='')

Bases: ete2.phylo.phylotree.PhyloNode

Re-implementation of the standart TreeNode instance. It adds attributes and methods to work with phylogentic trees.

Parameters:

• newick – path to tree in newick format, can also be a string
• alignment – path to alignment, can also be a string.
• alg_format (fasta) – alignment format.
• sp_naming_function – function to infer species name.
• format – type of newick format
• binpath – path to binaries, in case codeml or SLR are not in global path.

change_dist_to_evol(evol, model, fill=False)

change dist/branch length of the tree to a given evolutionary variable (dN, dS, w or bL), default is bL.

Parameters:

• evol – evolutionary variable
• model – Model object from which to retrieve evolutionary variables
• fill (False) – do not affects only dist parameter, each node will be annotated with all evolutionary variables (nodel.dN, node.w...).

get_descendant_by_node_id(idname)

returns node list corresponding to a given idname

get_evol_model(modelname)

returns one precomputed model

Parameters:modelname – string of the name of a model object stored Returns:Model object

get_most_likely(altn, null)

Returns pvalue of LRT between alternative model and null model.

usual comparison are:

Alternative	Null	Test
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	foreground branch not neutral (w != 1) RX if P<0.05 (means that w on frg=1) PS if P>0.05 and wfrg>1 CN if P>0.05 and wfrg>1 (Yang Nielsen 2002)
b_free	M0	different ratio on branches (Yang Nielsen 2002)

Parameters:

• altn – model with higher number of parameters (np)
• null – model with lower number of parameters (np)

link_to_alignment(alignment, alg_format='paml', nucleotides=True, **kwargs)

same function as for phyloTree, but translate sequences if nucleotides nucleotidic sequence is kept under node.nt_sequence

Parameters:

• alignment (True) – path to alignment or string
• alg_format – one of fasta phylip or paml
• alignment – set to False in case we want to keep it untranslated

link_to_evol_model(path, model)

link EvolTree to evolutionary model

• free-branch model (‘fb’) will append evol values to tree
• Site models (M0, M1, M2, M7, M8) will give evol values by site and likelihood

Parameters:

• path – path to outfile containing model computation result
• model – either the name of a model, or a Model object (usually empty)

mark_tree(node_ids, verbose=False, **kargs)

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"])

Parameters:

• node_ids – list of node ids (have a look to node.node_id)
• verbose (False) – warn if marks do not correspond to codeml standard
• kargs – mainly for the marks key-word which needs a list of marks (marks=[‘#1’, ‘#2’])

render(file_name, layout=None, w=None, h=None, tree_style=None, header=None, histfaces=None)

call super show adding up and down faces

Parameters:

• layout – a layout function
• tree_style (None) – tree_style object
• Nonehistface – an histogram face function. This is only to plot selective pressure among sites

run_model(model_name, ctrl_string='', keep=True, **kwargs)

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
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

Parameters:

• model_name – a string like “model-name[.some-secondary-name]” (e.g.: “fb.my_first_try”, or just “fb”) * model-name is compulsory, is the name of the model (see table above for the full list) * the second part is accessory, it is to avoid over-writing models with the same name.
• ctrl_string – list of parameters that can be used as control file.
• kwargs – extra parameters should be one of: verbose, CodonFreq, ncatG, cleandata, fix_blength, NSsites, fix_omega, clock, seqfile, runmode, fix_kappa, fix_alpha, Small_Diff, method, Malpha, aaDist, RateAncestor, outfile, icode, alpha, seqtype, omega, getSE, noisy, Mgene, kappa, treefile, model, ndata.

sep = '\n'

show(layout=None, tree_style=None, histfaces=None)

call super show of PhyloTree histface should be a list of models to be displayes as histfaces

Parameters:

• layout – a layout function
• tree_style (None) – tree_style object
• Nonehistface – an histogram face function. This is only to plot selective pressure among sites

write(features=None, outfile=None, format=10)

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:

Parameters:

• features – a list of feature names to be exported using the Extended Newick Format (i.e. features=[“name”, “dist”]). Use an empty list to export all available features in each node (features=[])
• outfile – writes the output to a given file
• format (10) – defines the newick standard used to encode the tree. See tutorial for details.
• format_root_node (False) – If True, it allows features and branch information from root node to be exported as a part of the newick text string. For newick compatibility reasons, this is False by default.
• is_leaf_fn – See TreeNode.traverse() for documentation.

Example:

t.get_newick(features=["species","name"], format=1)

EvolTree

alias of EvolNode