SPECIES FOR WHICH ORTHOLOGOUS EXONS ARE AVAILABLE

EUARCHONTOGLIRES
Homo_sapiens	Human	v1
Pan_troglodytes	Chimp	v1
Macaca_mulatta	Macaque	v1
Otolemur_garnettii	Bushbaby	v2
Microcebus_murinus	Mouse lemur	v2
Tupaia_belangeri	Tree shrew	v2
Mus_musculus	Mouse	v1
Rattus_norvegicus	Rat	v1
Cavia_porcellus	Guinea pig	v2
Spermophilus_tridecemlineatus	Ground squirrel	v2
Oryctolagus_cuniculus	Rabbit	v1
Ochotona_princeps	Pika	v2
LAURASIATHERIA
Bos_taurus	Cow	v1
Canis_familiaris	Dog	v1
Felis_catus	Cat	v2
Myotis_lucifugus	Microbat	v2
Erinaceus_europaeus	Hedgehog	v2
Sorex_araneus	Shrew	v2
AFROTHERIA
Loxodonta_africana	Elephant	v1
Echinops_telfairi	Tenrec	v1
XENARTHRA
Dasypus_novemcinctus	Armadillo	v1
MARSUPIALIA
Monodelphis_domestica	Opossum	v1
MONOTREMATA
Ornithorhynchus_anatinus	Platypus	v2

OrthoMaM exons are selected for a minimum of 6 species and a maximum of 23 species.

OrthoMaM mean = 14 ; standard-error = 3

RELATIVE EVOLUTIONARY RATE

The utility of a phylogenetic marker can be described by its relative evolutionary rate:
faster (respectively slower) evolving markers will be more suitable
for lower (respectively deeper) taxonomic levels.

In a first approximation, the total branch length (TBL) of the highest-likelihood tree
is a reasonable descriptor of the evolutionary rate of a given exon.
However, the TBL will preclude fair comparisons among different exons
when the taxon sampling differs: the higher the species number, the longer the TBL.

To circumvent this problem, we use the Super Distance Matrix (SDM) approach [Criscuolo et al. 2006],
with a three-step procedure:

	(i) 	The ML tree inferred from each of the 4,155 exons is converted
			into a matrix of additive distances by computing the path-length
			between each pair of species.
	(ii)	Each of the 4,155 matrices is brought closer to the others by a factor (αp),
			according to the least-squares criterion.
			This operation is equivalent to multiplying by αp every branch length
			of the initial trees.
	(iii)	Optimal values of the alpha_p parameters are calculated following Criscuolo et al. (2006),
			As αp are inversely proportional to the evolutionary rates,
			1/αp values provide a measure of rate heterogeneities among exons
			even if the number of taxa differs.

Exon-specific evolutionary rates are provided as relative values ranging from 0 to 2.8.

For example, if exons X and Y are respectively characterized by relative rates
rX = 0.2 and rY = 2.0, this means that Y is evolving 10 times faster than X.

Relative evolutionary rate SDM estimates here range from 0.02 to 2.8
OrthoMaM mean = 1.4 ; standard-error = 0.7

Reference:	Criscuolo A., Berry V., Douzery E. J. P. & Gascuel O., 2006.
			SDM: a fast distance-based approach for (super)tree building in phylogenomics.
			Systematic Biology 55 (5) : 740-755.

α SHAPE OF THE Γ DISTRIBUTION

The substitution rate heterogeneity among sites of the exon alignment
is described by the Γ distribution.

Lower (respectively higher) α values correspond to strong (respectively weak)
heterogeneity. If α > 1, the substitution pattern among sites is rather homogeneous.

α estimates here range from 0.01 to 5.0.
OrthoMaM mean = 0.6 ; standard-error = 0.6

Reference:	Yang Z., 1996.
			Among-site rate variation and its impact on phylogenetic analyses.
			Trends in Ecology and Evolutin 11 (9) : 367-372.

PERCENTAGE OF G+C ON THIRD CODON POSITIONS

This parameter is a descriptor of the degree of base composition heterogeneity.
It is more contrasted on third codon positions than on the whole exon.

%GC3 estimates here range from 22% to 96%
OrthoMaM mean = 66% ; standard-error = 15%