Available substitution models
Substitution model types¶
Assign the value in the "Abbreviation" column as a string to the submod_type parameter, e.g.
submod_type="GTR"
In [1]:
Copied!
from piqtree import available_models
available_models()
from piqtree import available_models
available_models()
Out[1]:
| Model Type | Abbreviation | Description |
|---|---|---|
| nucleotide | JC | Equal substitution rates and equal base frequencies (Jukes and Cantor, 1969). |
| nucleotide | JC69 | Equal substitution rates and equal base frequencies (Jukes and Cantor, 1969). |
| nucleotide | F81 | Equal rates but unequal base freq. (Felsenstein, 1981). |
| nucleotide | K80 | Unequal transition/transversion rates and equal base freq. (Kimura, 1980). |
| nucleotide | K2P | Unequal transition/transversion rates and equal base freq. (Kimura, 1980). |
| nucleotide | HKY | Unequal transition/transversion rates and unequal base freq. (Hasegawa, Kishino and Yano, 1985). |
| nucleotide | HKY85 | Unequal transition/transversion rates and unequal base freq. (Hasegawa, Kishino and Yano, 1985). |
| nucleotide | TN | Like HKY but unequal purine/pyrimidine rates (Tamura and Nei, 1993). |
| nucleotide | TN93 | Like HKY but unequal purine/pyrimidine rates (Tamura and Nei, 1993). |
| nucleotide | TNe | Like TN but equal base freq. |
| nucleotide | K81 | Three substitution types model and equal base freq. (Kimura, 1981). |
| nucleotide | K3P | Three substitution types model and equal base freq. (Kimura, 1981). |
| nucleotide | K81u | Like K81 but unequal base freq. |
| nucleotide | TPM2 | AC=AT, AG=CT, CG=GT and equal base freq. |
| nucleotide | TPM2u | Like TPM2 but unequal base freq. |
| nucleotide | TPM3 | AC=CG, AG=CT, AT=GT and equal base freq. |
| nucleotide | TPM3u | Like TPM3 but unequal base freq. |
| nucleotide | TIM | Transition model, AC=GT, AT=CG and unequal base freq. |
| nucleotide | TIMe | Like TIM but equal base freq. |
| nucleotide | TIM2 | AC=AT, CG=GT and unequal base freq. |
| nucleotide | TIM2e | Like TIM2 but equal base freq. |
| nucleotide | TIM3 | AC=CG, AT=GT and unequal base freq. |
| nucleotide | TIM3e | Like TIM3 but equal base freq. |
| nucleotide | TVM | Transversion model, AG=CT and unequal base freq. |
| nucleotide | TVMe | Like TVM but equal base freq. |
| nucleotide | SYM | Symmetric model with unequal rates but equal base freq. (Zharkikh, 1994). |
| nucleotide | GTR | General time reversible model with unequal rates and unequal base freq. (Tavare, 1986). |
| nucleotide | STRSYM | Strand-symmetric model (Bielawski and Gold, 2002). |
| nucleotide | UNREST | Unrestricted model. |
| nucleotide | 1.1 | Reversible model. Equal base frequencies. equiv. to JC |
| nucleotide | 2.2b | Reversible model. Equal base frequencies. equiv. to K2P |
| nucleotide | 3.3a | Reversible model. Equal base frequencies. equiv. to K3P |
| nucleotide | 3.3b | Non-reversible model. Equal base frequencies. |
| nucleotide | 3.3c | Reversible model. Equal base frequencies. equiv. to TNe |
| nucleotide | 3.4 | Reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 4.4a | Reversible model. Unconstrained base frequencies. equiv. to F81 |
| nucleotide | 4.4b | Reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 4.5a | Non-reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 4.5b | Non-reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 5.6a | Non-reversible model. Equal base frequencies. |
| nucleotide | 5.6b | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 5.7a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). |
| nucleotide | 5.7b | Non-reversible model. Equal base frequencies. |
| nucleotide | 5.7c | Non-reversible model. Equal base frequencies. |
| nucleotide | 5.11a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). |
| nucleotide | 5.11b | Non-reversible model. Equal base frequencies. |
| nucleotide | 5.11c | Non-reversible model. Equal base frequencies. |
| nucleotide | 5.16 | Non-reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 6.6 | Non-reversible model. f(A)=f(G) and f(C)=f(T). equiv. to STRSYM for strand-symmetric model (Bielawski and Gold, 2002) |
| nucleotide | 6.7a | Non-reversible model. Unconstrained base frequencies. F81+K3P |
| nucleotide | 6.7b | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 6.8a | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 6.8b | Non-reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 6.17a | Non-reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 6.17b | Non-reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 8.8 | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 8.10a | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 8.10b | Non-reversible model. f(A)=f(G) and f(C)=f(T). |
| nucleotide | 8.16 | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 8.17 | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 8.18 | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 9.20a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). |
| nucleotide | 9.20b | Non-reversible model. Equal base frequencies. Doubly stochastic |
| nucleotide | 10.12 | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 10.34 | Non-reversible model. Unconstrained base frequencies. |
| nucleotide | 12.12 | Non-reversible model. Unconstrained base frequencies. equiv. to UNREST (unrestricted model) |
| nucleotide | RY1.1 | Reversible model. Equal base frequencies. equiv. to JC Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY2.2b | Reversible model. Equal base frequencies. equiv. to K2P Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY3.3a | Reversible model. Equal base frequencies. equiv. to K3P Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY3.3b | Non-reversible model. Equal base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY3.3c | Reversible model. Equal base frequencies. equiv. to TNe Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY3.4 | Reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY4.4a | Reversible model. Unconstrained base frequencies. equiv. to F81 Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY4.4b | Reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY4.5a | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY4.5b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.6a | Non-reversible model. Equal base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.6b | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.7a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.7b | Non-reversible model. Equal base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.7c | Non-reversible model. Equal base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.11a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.11b | Non-reversible model. Equal base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.11c | Non-reversible model. Equal base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY5.16 | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY6.6 | Non-reversible model. f(A)=f(G) and f(C)=f(T). equiv. to STRSYM for strand-symmetric model (Bielawski and Gold, 2002) Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY6.7a | Non-reversible model. Unconstrained base frequencies. F81+K3P Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY6.7b | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY6.8a | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY6.8b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY6.17a | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY6.17b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY8.8 | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY8.10a | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY8.10b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY8.16 | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY8.17 | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY8.18 | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY9.20a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY9.20b | Non-reversible model. Equal base frequencies. Doubly stochastic Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY10.12 | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY10.34 | Non-reversible model. Unconstrained base frequencies. Pairing: purine-pyrimidine pairing (default). |
| nucleotide | RY12.12 | Non-reversible model. Unconstrained base frequencies. equiv. to UNREST (unrestricted model) Pairing: purine-pyrimidine pairing (default). |
| nucleotide | WS1.1 | Reversible model. Equal base frequencies. equiv. to JC Pairing: weak-strong pairing. |
| nucleotide | WS2.2b | Reversible model. Equal base frequencies. equiv. to K2P Pairing: weak-strong pairing. |
| nucleotide | WS3.3a | Reversible model. Equal base frequencies. equiv. to K3P Pairing: weak-strong pairing. |
| nucleotide | WS3.3b | Non-reversible model. Equal base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS3.3c | Reversible model. Equal base frequencies. equiv. to TNe Pairing: weak-strong pairing. |
| nucleotide | WS3.4 | Reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS4.4a | Reversible model. Unconstrained base frequencies. equiv. to F81 Pairing: weak-strong pairing. |
| nucleotide | WS4.4b | Reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS4.5a | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS4.5b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS5.6a | Non-reversible model. Equal base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS5.6b | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS5.7a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: weak-strong pairing. |
| nucleotide | WS5.7b | Non-reversible model. Equal base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS5.7c | Non-reversible model. Equal base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS5.11a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: weak-strong pairing. |
| nucleotide | WS5.11b | Non-reversible model. Equal base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS5.11c | Non-reversible model. Equal base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS5.16 | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS6.6 | Non-reversible model. f(A)=f(G) and f(C)=f(T). equiv. to STRSYM for strand-symmetric model (Bielawski and Gold, 2002) Pairing: weak-strong pairing. |
| nucleotide | WS6.7a | Non-reversible model. Unconstrained base frequencies. F81+K3P Pairing: weak-strong pairing. |
| nucleotide | WS6.7b | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS6.8a | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS6.8b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS6.17a | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS6.17b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS8.8 | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS8.10a | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS8.10b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: weak-strong pairing. |
| nucleotide | WS8.16 | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS8.17 | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS8.18 | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS9.20a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: weak-strong pairing. |
| nucleotide | WS9.20b | Non-reversible model. Equal base frequencies. Doubly stochastic Pairing: weak-strong pairing. |
| nucleotide | WS10.12 | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS10.34 | Non-reversible model. Unconstrained base frequencies. Pairing: weak-strong pairing. |
| nucleotide | WS12.12 | Non-reversible model. Unconstrained base frequencies. equiv. to UNREST (unrestricted model) Pairing: weak-strong pairing. |
| nucleotide | MK1.1 | Reversible model. Equal base frequencies. equiv. to JC Pairing: aMino-Keto pairing |
| nucleotide | MK2.2b | Reversible model. Equal base frequencies. equiv. to K2P Pairing: aMino-Keto pairing |
| nucleotide | MK3.3a | Reversible model. Equal base frequencies. equiv. to K3P Pairing: aMino-Keto pairing |
| nucleotide | MK3.3b | Non-reversible model. Equal base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK3.3c | Reversible model. Equal base frequencies. equiv. to TNe Pairing: aMino-Keto pairing |
| nucleotide | MK3.4 | Reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK4.4a | Reversible model. Unconstrained base frequencies. equiv. to F81 Pairing: aMino-Keto pairing |
| nucleotide | MK4.4b | Reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK4.5a | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK4.5b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK5.6a | Non-reversible model. Equal base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK5.6b | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK5.7a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK5.7b | Non-reversible model. Equal base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK5.7c | Non-reversible model. Equal base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK5.11a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK5.11b | Non-reversible model. Equal base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK5.11c | Non-reversible model. Equal base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK5.16 | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK6.6 | Non-reversible model. f(A)=f(G) and f(C)=f(T). equiv. to STRSYM for strand-symmetric model (Bielawski and Gold, 2002) Pairing: aMino-Keto pairing |
| nucleotide | MK6.7a | Non-reversible model. Unconstrained base frequencies. F81+K3P Pairing: aMino-Keto pairing |
| nucleotide | MK6.7b | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK6.8a | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK6.8b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK6.17a | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK6.17b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK8.8 | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK8.10a | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK8.10b | Non-reversible model. f(A)=f(G) and f(C)=f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK8.16 | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK8.17 | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK8.18 | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK9.20a | Non-reversible model. f(A)+f(G)=0.5=f(C)+f(T). Pairing: aMino-Keto pairing |
| nucleotide | MK9.20b | Non-reversible model. Equal base frequencies. Doubly stochastic Pairing: aMino-Keto pairing |
| nucleotide | MK10.12 | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK10.34 | Non-reversible model. Unconstrained base frequencies. Pairing: aMino-Keto pairing |
| nucleotide | MK12.12 | Non-reversible model. Unconstrained base frequencies. equiv. to UNREST (unrestricted model) Pairing: aMino-Keto pairing |
| protein | Blosum62 | BLOcks SUbstitution Matrix (Henikoff and Henikoff, 1992). Note that BLOSUM62 is not recommended for phylogenetic analysis as it was designed mainly for sequence alignments. |
| protein | cpREV | chloroplast matrix (Adachi et al., 2000). |
| protein | Dayhoff | General matrix (Dayhoff et al., 1978). |
| protein | DCMut | Revised Dayhoff matrix (Kosiol and Goldman, 2005). |
| protein | EAL | General matrix. To be used with profile mixture models (for eg. EAL+C60) for reconstructing relationships between eukaryotes and Archaea (Banos et al., 2024). |
| protein | ELM | General matrix. To be used with profile mixture models (for eg. ELM+C60) for phylogenetic analysis of proteins encoded by nuclear genomes of eukaryotes (Banos et al., 2024). |
| protein | FLAVI | Flavivirus (Le and Vinh, 2020). |
| protein | FLU | Influenza virus (Dang et al., 2010). |
| protein | GTR20 | General time reversible models with 190 rate parameters. |
| protein | HIVb | HIV between-patient matrix HIV-Bm (Nickle et al., 2007). |
| protein | HIVw | HIV within-patient matrix HIV-Wm (Nickle et al., 2007). |
| protein | JTT | General matrix (Jones et al., 1992). |
| protein | JTTDCMut | Revised JTT matrix (Kosiol and Goldman, 2005). |
| protein | LG | General matrix (Le and Gascuel, 2008). |
| protein | mtART | Mitochondrial Arthropoda (Abascal et al., 2007). |
| protein | mtMAM | Mitochondrial Mammalia (Yang et al., 1998). |
| protein | mtREV | Mitochondrial Vertebrate (Adachi and Hasegawa, 1996). |
| protein | mtZOA | Mitochondrial Metazoa (Animals) (Rota-Stabelli et al., 2009). |
| protein | mtMet | Mitochondrial Metazoa (Vinh et al., 2017). |
| protein | mtVer | Mitochondrial Vertebrate (Vinh et al., 2017). |
| protein | mtInv | Mitochondrial Invertebrate (Vinh et al., 2017). |
| protein | NQ.bird | Non-reversible Q matrix (Dang et al., 2022) estimated for birds (Jarvis et al., 2015). |
| protein | NQ.insect | Non-reversible Q matrix (Dang et al., 2022) estimated for insects (Misof et al., 2014). |
| protein | NQ.mammal | Non-reversible Q matrix (Dang et al., 2022) estimated for mammals (Wu et al., 2018). |
| protein | NQ.pfam | General non-reversible Q matrix (Dang et al., 2022) estimated from Pfam version 31 database (El-Gebali et al., 2018). |
| protein | NQ.plant | Non-reversible Q matrix (Dang et al., 2022) estimated for plants (Ran et al., 2018). |
| protein | NQ.yeast | Non-reversible Q matrix (Dang et al., 2022) estimated for yeasts (Shen et al., 2018). |
| protein | Poisson | Equal amino-acid exchange rates and frequencies. |
| protein | PMB | Probability Matrix from Blocks, revised BLOSUM matrix (Veerassamy et al., 2004). |
| protein | Q.bird | Q matrix (Minh et al., 2021) estimated for birds (Jarvis et al., 2015). |
| protein | Q.insect | Q matrix (Minh et al., 2021) estimated for insects (Misof et al., 2014). |
| protein | Q.mammal | Q matrix (Minh et al., 2021) estimated for mammals (Wu et al., 2018). |
| protein | Q.pfam | General Q matrix (Minh et al., 2021) estimated from Pfam version 31 database (El-Gebali et al., 2018). |
| protein | Q.plant | Q matrix (Minh et al., 2021) estimated for plants (Ran et al., 2018). |
| protein | Q.yeast | Q matrix (Minh et al., 2021) estimated for yeasts (Shen et al., 2018). |
| protein | rtREV | Retrovirus (Dimmic et al., 2002). |
| protein | VT | General 'Variable Time' matrix (Mueller and Vingron, 2000). |
| protein | WAG | General matrix (Whelan and Goldman, 2001). |
215 rows x 3 columns