Evolutionary model
Option: --model STRING | FILE (mandatory)
Evolutionary model can be specified globally (i.e., for the whole alignment), or multiple models can be selected for different subsets of alignment columns (so called partitioned analysis).
Single model
Global per-alignment evolutionary model can be given as a string on the command line.
Model specification always starts with a substitution matrix name, e.g., GTR for DNA data or LG for protein data.
Several optional modifiers can be added, separated by + and in arbitrary order.
NOTE: all per-state values (e.g. base frequencies) must be given in the following order.
All substitution matrices and modifiers are summarized in the following table:
| Modifier | Possible values |
|---|---|
| Substitution matrix |
DNA data: JC, K80, F81, HKY, TN93ef, TN93, K81, K81uf, TPM2, TPM2uf, TPM3, TPM3uf, TIM1, TIM1uf, TIM2, TIM2uf, TIM3, TIM3uf,TVMef, TVM, SYM, GTRProtein data*: Blosum62, cpREV, Dayhoff, DCMut, DEN, FLU, HIVb,HIVw, JTT, JTT-DCMut, LG, mtART,mtMAM, mtREV, mtZOA, PMB, rtREV,stmtREV, VT, WAG, LG4M (implies +G4), LG4X (implies +R4), PROTGTR Binary data (0/1): BIN Morphological/multistate: MULTIx_MK, MULTIx_GTR (where x = number of states, e.g.: MULTI8_MK for a 8-state model with equal rates) state encoding Unphased diploid genotypes (10 states): GTJC GTHKY4 GTGTR4 GTGTR Fixed user-defined rates: e.g. HKY{1.0/2.5} or GTR{0.5/2.0/1.0/1.2/0.1/1.0} or PROTGTR{rates.txt}. The rates above define upper triangle of the substitution matrix, e.g. for GTR the order is A-C, A-G, A-T, C-G, C-T, G-T |
| Stationary frequencies | +F or +FC (empirical)+FO (ML estimate)+FE (equal) +FU{f1/f2/../fn} (user-defined: f1 f2 ... fn) +FU{freqs.txt} (user-defined from file) |
| Proportion of invariant sites |
+I or +IO (ML estimate)+IC (empirical)+IU{p} (user-defined: p) |
| Among-site rate heterogeneity model |
+G (discrete GAMMA with 4 categories, mean category rates, ML estimate of alpha) +GA (as above, but with median category rates) +Gn (discrete GAMMA with n categories, ML estimate of alpha) +Gn{a} (discrete GAMMA with n categories and user-defined alpha a) +Rn (FreeRate with n categories, ML estimate of rates and weights) +Rn{r1/r2/../rn}{w1/w2/../wn} (FreeRate with n categories, user-defined rates r1 r2 ... rn and weights w1 w2 ... wn) |
| Ascertainment bias correction |
+ASC_LEWIS (Lewis’ method)+ASC_FELS{w} (Felsenstein’s method with total number of invariable sites w)+ASC_STAM{w1/w2/../wn} (Stamatakis’ method with per-state invariable site numbers w1 w2 ... wn) |
| Custom character-to-state mapping |
+M{statechars}{gapchars} e.g. MULTI6_GTR+M{ABCDEF}{X-?}+Mi{statechars}{gapchars} same as above, but statechars are case-insensitive+M{charmap.txt} mapping defined in charmap.txt file (see below) |
* see libpll wiki for details & references
Multiple models
Multiple models can be defined in a RAxML-style partition file. Example:
JC+G, p1 = 1-100, 252-400
HKY+F, p2 = 101-180, 251
GTR+I, p3 = 181-250
Here, each line defines a partition and consist of three elements:
- model specification (see above)
- partition name
- range of alignment columns
Branch length linkage
In case of partitioned analysis, three branch length estimation modes are available:
| Command | Meaning |
|---|---|
--brlen linked |
Branch lengths are identical for all partitions |
--brlen scaled |
(default) Joint branch length estimation with individual per-partition scalers (i.e., branch lengths are proportional) |
--brlen unlinked |
Branch lengths are estimated independently for each partition (cf. RAxML -M option) |
State encoding & order
Defaults
|Data type| Order |
|———|——-|
|DNA | A C G T |
|PROTEIN | A R N D C Q E G H I L K M F P S T W Y V |
|MULTISTATE | 0 1 2 3 4 5 6 7 8 9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z ! " # $ % & ' ( ) * + , / : ; < = > @ [ \ ] ^ _ { \| } ~ |
|GENOTYPE (diploid unphased) | A C G T M R W S Y K
(Meaning: A/A C/C G/G T/T A/C A/G A/T C/G C/T G/T) |
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