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codeML (version 4.9+galaxy2)
The fasta file with the sequences to be analyzed
Tree file in Newick format
Advanced Options
Advanced Options 0

Galaxy integration Victor Mataigne and ABIMS TEAM.

Contact for any questions or concerns about the Galaxy implementation of this tool.

CompCodeML (from paml package)

A few help is detailed below ; full and detailed codeml readme can be found on the paml website.

Due to their high number, some parameters incompatibility can remain.

This Galaxy implementation :

We recommand to have a look at the full paml manual before looking at the advanced parameters, in order to spot parameters incompatibilities and to know what each model does. If you choose by mistake incompatible parameters, the output files will be empty, except the log file ("run_codeml" output) which will normally explicit the error.

Known incompatibilities:


codeML finds positive selection within branches or codons within a tree and a set of sequences.

Input files


Several models are available.

Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml.

Branch models allow the omega ratio to vary among branches in the phylogeny and are useful for detecting positive selection acting on particular lineages. Sites models allow the omega ratio to vary among sites (codons or amino acids).

Two pairs of models appear to be particularly useful, forming two likelihood ratio tests of positive selection. The first compares M1a ('NearlyNeutral', NSsites=1) and M2a ('PositiveSelection', NSsites=2), while the second compares M7 ('beta', NSsites=7) and M8 ('beta&ω', NSsites=8).

Other examples of model

How to run the branch-site models (A & B in Yang & Nielsen 2002 MBE) ? The options are :

How to run the M0 (one-ratio) model :

model = 0, NSsites= = 0.

Advanced Parameters

See paml complete manual and FAQ on the paml website.

Details of some parameters :

Output files

How to edit manually the tree file : Branch or node labels

Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest.

In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); :
The internal branch ancestral to human and gibbon has the ratio ω1, while all other branches (with the default label #0) have the background ratio ω0.

The following trees are equivalent: - ((rabbit, rat) $1, human), goat_cow, marsupial); - (((rabbit #1, rat #1) #1, human), goat_cow, marsupial);

$ is the symbol for clade labels.

Rules concerning nested clade labels : The symbol # takes precedence over the symbol $, and clade labels close to the tips take precedence over clade labels for ancestral nodes close to the root.

In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); :
$1 is first applied to the whole clade of placental mammals (except for the human lineage), and then $2 is applied to the rabbit-rat clade. Equivalent tree with only '#' : ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial);