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SPECIES FOR WHICH ORTHOLOGOUS EXONS / CDS ARE AVAILABLE
EUARCHONTOGLIRES
Homo_sapiensHumanv1
Pan_troglodytesChimpv1
Gorilla_gorillaGorillav5
Pongo_pygmaeusOrangutanv3
Macaca_mulattaMacaquev1
Tarsius_syrichtaTarsierv5
Otolemur_garnettii Bushbabyv2
Microcebus_murinusMouse lemurv2
Tupaia_belangeriTree shrewv2
Mus_musculusMousev1
Rattus_norvegicusRatv1
Dipodomys_ordiiKangaroo ratv5
Cavia_porcellusGuinea pigv2
Spermophilus_tridecemlineatusGround squirrelv2
Oryctolagus_cuniculusRabbitv1
Ochotona_princepsPikav2
LAURASIATHERIA
Bos_taurusCowv1
Vicugna_pacosAlpacav5
Tursiops_truncatusDolphinv5
Equus_caballusHorsev3
Canis_familiarisDogv1
Felis_catusCatv2
Myotis_lucifugusMicrobatv2
Pteropus_vampyrusMegabatv5
Erinaceus_europaeusHedgehogv2
Sorex_araneusShrewv2
AFROTHERIA
Loxodonta_africanaElephantv1
Procavia_capensisHyraxv5
Echinops_telfairiTenrecv1
XENARTHRA
Dasypus_novemcinctusArmadillov1
Choloepus_hoffmanniSlothv5
MARSUPIALIA
Monodelphis_domesticaOpossumv1
MONOTREMATA
Ornithorhynchus_anatinusPlatypus
v2






RELATIVE EVOLUTIONARY RATE_
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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.
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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.
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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 exons / CDS is converted into a matrix of additive distances by computing the path-length between each pair of species.
	(ii)	Each of the 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 / CDS even if the number of taxa differs.
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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.
	
	
	
	
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.