"Custom","Custom 4x4 reversible model (defined as in 010023) with choice of several equilibrium frequencies options.","4","nucleotide","custm4x4.mdl";
"Custom_AA","Custom 20x20 reversible model (read from a file).","20","aminoacid","Custom_AA.mdl";
"Custom_Empirical","Custom 20x20 empirical reversible model (read from a file).","20","aminoacid","Custom_AA_empirical.mdl";
"Dayhoff","Dayfoff model for amino-acids","20","aminoacid","Dayhoff.mdl";
"Dayhoff+F","Dayfoff model for amino-acids with empirical character frequencies","20","aminoacid","Dayhoff_F.mdl";
"EqualInput","Equal input model for amino-acids","20","aminoacid","EIAA.mdl";
"Empirical Protein","Select from a collection of empricial protein models","20","aminoacid","Empirical.mdl";
"WAG","Whelan-Goldman model for amino-acids","20","aminoacid","WAG.mdl";
"WAG+F","Whelan-Goldman model for amino-acids  with empirical character frequencies","20","aminoacid","WAG_F.mdl";
"Jones","Jones et al Model (based on SWISSPROT Version 22 data)","20","aminoacid","Jones.mdl";
"Jones+F","Jones Model (based on SWISSPROT Version 22 data) with empirical character frequencies","20","aminoacid","Jones_F.mdl";
"Fitness","Fitness based model (Goldstein et al)","20","aminoacid","fitness.mdl";
"rtREV","Matrix optimized for viral pol genes (specifically, reverse transcriptase). Dimmic et al JME (2002)55:65-73,","20","aminoacid","rtREV.mdl";
"rtREV+F","Matrix optimized for viral pol genes (specifically, reverse transcriptase) with empirical character frequencies. Dimmic et al JME (2002)55:65-73,","20","aminoacid","rtREV_F.mdl";
"REV","General Reversible model (189+branch lengths parameters!)","20","aminoacid","mtREV.mdl";
"RedREV","General Reversible model reduced to allow non-zero rates only between a.a. separataed by a single nucleotide substitution","20","aminoacid","reducedREV.mdl";
"F81","Felsenstein 81 (F81).Rate heterogeneity (and HM spatial correlation) optional.","4","nucleotide","F81.mdl";
"F81B","Felsenstein 81 (F81) for binary data. Rate heterogeneity (and HM spatial correlation) optional.","2","binary","F81_binary.mdl";
"F84","Felsenstein 84. Rate heterogeneity (and HM spatial correlation) optional.","4","nucleotide","F84.mdl";
"F84P","Felsenstein 84, compatible with PHYLIP's dnaml version. User chooses ts/tv ratio. Rate heterogeneity (and HM spatial correlation) optional.","4","nucleotide","F84P.mdl";
"GRM","General Reversible Model.Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).","4","nucleotide","GRM.mdl";
"GY94","Goldman-Yang 94 codon model. Shared or independent dS/dN Possible Rate heterogeneity (and HM spatial correlation).","*","codon","GY94.mdl";
"GY94w9","Goldman-Yang 94 codon model with nucleotide equilibrium frequencies varying based on their position in the codon (6 extra parameters). Shared or independent dS/dN Possible Rate heterogeneity (and HM spatial correlation).","*","codon","GY94w9.mdl";
"GY94customF3x4","Goldman-Yang 94 codon model crossed with an arbitrary nucleotide model and the F3x4 frequency estimator. Shared or independent dS/dN Possible Rate heterogeneity (and HM spatial correlation).","*","codon","GY94customF3x4.mdl";
"HKY85","Hasegawa et al.,1985. Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).","4","nucleotide","HKY85.mdl";
"JC69","Jukes-Cantor 1969. Rate heterogeneity (and HM spatial correlation) optional.","4","nucleotide","JC69.mdl";
"JC69B","Jukes-Cantor 1969 for binary data. Rate heterogeneity (and HM spatial correlation) optional.","2","binary","JC69_binary.mdl";
"K2P","Kimura 2 parameter (K2P).Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).","4","nucleotide","K2P.mdl";
"K3ST","Kimura(1981) 3 substitution type model. Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).","4","nucleotide","K3ST.mdl";
"MG94","Muse-Gaut 94 codon model. Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94.mdl";
"MG94x2","Muse-Gaut 94+custom nucleotide biases codon model. Separate rate heterogeneity distributions for synonymous and non-synonymous changes.","*","codon","MG94x2.mdl";
"MG94w9","Muse-Gaut 94 codon model with nucleotide equilibrium frequencies varying based on their position in the codon (6 extra parameters). Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94with9freqs.mdl";
"MG94custom","Muse-Gaut 94 crossed with a nucleotide substituion model. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94custom.mdl";
"MG94customFreqs","Muse-Gaut 94 crossed with a nucleotide substituion model; 9 frequency parameters(positional nucleotide frequencies) are estimated from the data. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94customFreqs.mdl";
"MG94customF1x4","Muse-Gaut 94 crossed with a nucleotide substituion model, using a simpler F1x4 codon frequency estimator. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94customF1x4.mdl";
"MG94customCF3x4","Muse-Gaut 94 crossed with a nucleotide substituion model, using a corrected CF3x4 codon frequency estimator. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94customCF3x4.mdl";
"MG94wAA","Muse-Gaut 94 crossed with a nucleotide substituion model AND several predefined non-synonymous substitution classes. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94wAA.mdl";
"MG94wAAUserFreqs","Muse-Gaut 94 crossed with a nucleotide substituion model AND several predefined non-synonymous substitution classes. 9 frequency parameters(positional nucleotide frequencies) are defined by user (i.e. you). Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94wAAUserFreqs.mdl";
"MG94wAAFreqs","Muse-Gaut 94 crossed with a nucleotide substituion model AND several predefined non-synonymous substitution classes. 9 frequency parameters(positional nucleotide frequencies) are estimated from the data. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94wAAFreqs.mdl";
"MG94wAAF61","Muse-Gaut 94 crossed with a nucleotide substituion model AND several predefined non-synonymous substitution classes. 61 codon frequency parameters are estimated in the model. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94wAAF61.mdl";
"MG94wAAF61Multiple","Muse-Gaut 94 crossed with a nucleotide substituion model, several predefined non-synonymous substitution classes AND 4 separate rates for 2 and 3 step synonynymous and non-synonymous substitutions. 61 codon frequency parameters are estimated in the model. Possible Rate heterogeneity (and HM spatial correlation).","*","codon","MG94wAAF61multiple.mdl";
"MG94wEX","Muse-Gaut 94 crossed with a nucleotide substituion model AND an acceptance bias based on the exhangeability metric by Stolzfus and Yampolsky.","*","codon","MG94wEX.mdl";
"ECM","Kosiol, Holmes and Goldman Empirical Codon model estimated from Pandit alignments (MBE 24:1464)","*","codon","ECM.mdl";
"ECM+F","Kosiol, Holmes & Goldman Empirical Codon model estimated from Pandit alignments with alignment specific F61 frequency parameters (MBE 24:1464)","*","codon","ECM+F.mdl";
"ECM+F+omega","Kosiol, Holmes & Goldman Empirical Codon model estimated from Pandit alignments with alignment specific F61 frequency parameters and dNdS parameter (MBE 24:1464)","*","codon","ECM+F+omega.mdl";
"ECM+MLFREQS","Kosiol, Holmes & Goldman Empirical Codon model estimated from Pandit alignments with 9 frequency parameters(positional nucleotide frequencies) estimated from the data.","*","codon","ECM+MLFREQS.mdl";
"ECM+F3x4","Kosiol, Holmes & Goldman Empirical Codon model estimated from Pandit alignments with F3x4 frequency estimator","*","codon","ECM+F3x4.mdl";
"LCAP","Linear Combination of Amino Acid Properties from Conant, Wagner and Stadler (MPE 42:298)","*","codon","LCAP.mdl";
"MEC","Mixed empirical and mechanistic codon model of Doron-Faigenboim and Pupko (MBE 24:388-397)","*","codon","MEC.mdl";
"NRM","Non reversible model, constrained to have observed counts as its equilibrium frequencies. 11 parameters (8 rate parameteres + 3 frequency parameters).","4","nucleotide","NRM.mdl";
"NRM+Freqs","Non reversible model, NOT constrained to have observed counts as its equilibrium frequencies. 11 parameters.","4","nucleotide","NRM+Freqs.mdl";
"TrN","Tamura and Nei 1993. Local or global parameters. Local or global parameters. Possible Rate heterogeneity (and HM spatial correlation).","4","nucleotide","TrN.mdl";
"HIVBetween","Between patient empricial model for HIV","20","aminoacid","HIVbetween.mdl";
"HIVBetween+F","Between patient empricial model for HIV with frequencies ","20","aminoacid","HIVbetween+F.mdl";
"HIVWithin","Within patient empricial model for HIV","20","aminoacid","HIVwithin.mdl";
"HIVWithin+F","Within patient empricial model for HIV with frequencies ","20","aminoacid","HIVwithin+F.mdl";
"mtMAM","Empirical model for mammalian mtDNA genes. Yang, Z., R. Nielsen, and M. Hasegawa.  1998.  Models of amino acid substitution and applications to Mitochondrial protein evolution, MBE 15:1600-1611.","20","aminoacid","mtMAM.mdl";
"mtMAM+F","Empirical model for mammalian mtDNA genes with emprically estimated base frequencies. Yang, Z., R. Nielsen, and M. Hasegawa.  1998.  Models of amino acid substitution and applications to Mitochondrial protein evolution, MBE 15:1600-1611.","20","aminoacid","mtMAM_F.mdl";
"mtREV 24","Empirical model for mtDNA genes. Yang, Z., R. Nielsen, and M. Hasegawa.  1998.  Models of amino acid substitution and applications to Mitochondrial protein evolution, MBE 15:1600-1611.","20","aminoacid","mtREV_24.mdl";
"mtREV 24+F","Empirical model for mtDNA genes with emprically estimated base frequencies. Adachi, J. and Hasegawa, M. (1996) MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood.  Computer Science Monographs of Institute of Statistical Mathematics 28:1-150.","20","aminoacid","mtREV_24_F.mdl";
"EX","Exchangeability metric by Stolzfus and Yampolsky.","20","aminoacid","EX.mdl";
"Muse95","Dinucleotide extension of HKY85. Basic model described in 'Evolutionary  Analyses of DNA Sequences  Subject  to Constraints on  Secondary  Structure' by Spencer V. Muse in Genetics 139 1429-1439  (March, 1995), augmented by site-to-site rate variation (optional).","16","dinucleotide","RNAMuse95.mdl";
"RNA16","Any particular class of the general reversible model, including some predefined models.","16","dinucleotide","RNA16.mdl";
"RNA16SvH","Any particular type of the REV model for nucleotides scaled to a 16x16 state space as in 'Toward Assigning Helical Regions in Alignments of Ribosomal RNA and Testing the Appropriateness of Evolutionary Models' by Michael Schoniger and Arndt von Haeseler, J Mol Evol (1999) 49:691Ð698.","16","dinucleotide","RNA16SvH.mdl";

