WAG matrix implementation

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I am working with certain programs in python3.4 (OS is windows). I want to use WAG matrix for phylogeny inference, but I am confused about the formula implemented by it.



For example, in phylogenetics study, when a sequence file is used to generate a distance based matrix, there is a formula called "p-distance" implemented and on the basis of this formula and some standard values for sequence data, a matrix is generated which is later used to construct a tree. When a character based method for tree construction is used, "WAG" is one of the matrices used for likelihood tree construction. What I want to say is that if one wants to implement this matrix, then what is the formula basis for it?




I have an aligned protein sequence file and I need to generate "WAG"
matrix from it. The thing is that I have been studying literature
regarding wag matrix but I could not get how does it perform
calculation??? Does it have a specific formula?? (For example,
'p-distance' is a formula used bu distance matrix) I want to give
aligned protein sequence file as input and have a matrix generated as
output.





matrices python




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  • Welcome to MSE. Please read this text about how to ask a good question.
    – José Carlos Santos
    Jul 30 at 9:33










  • Do I need to rephrase my question??
    – Sidra Younas
    Jul 30 at 9:35










  • I think that it would be in your best interest to add more details.
    – José Carlos Santos
    Jul 30 at 9:36










  • Alright then, I have an aligned protein sequence file and I need to generate "WAG" matrix from it. The thing is that I have been studying literature regarding wag matrix but I could not get how does it perform calculation??? Does it have a specific formula?? (For example, 'p-distance' is a formula used bu distance matrix) I want to give aligned protein sequence file as input and have a matrix generated as output.
    – Sidra Younas
    Jul 30 at 9:40











  • What I meant was that perhaps that you could edit your question.
    – José Carlos Santos
    Jul 30 at 9:41














up vote
0
down vote

favorite












I am working with certain programs in python3.4 (OS is windows). I want to use WAG matrix for phylogeny inference, but I am confused about the formula implemented by it.



For example, in phylogenetics study, when a sequence file is used to generate a distance based matrix, there is a formula called "p-distance" implemented and on the basis of this formula and some standard values for sequence data, a matrix is generated which is later used to construct a tree. When a character based method for tree construction is used, "WAG" is one of the matrices used for likelihood tree construction. What I want to say is that if one wants to implement this matrix, then what is the formula basis for it?




I have an aligned protein sequence file and I need to generate "WAG"
matrix from it. The thing is that I have been studying literature
regarding wag matrix but I could not get how does it perform
calculation??? Does it have a specific formula?? (For example,
'p-distance' is a formula used bu distance matrix) I want to give
aligned protein sequence file as input and have a matrix generated as
output.





matrices python




share|cite|improve this question





















  • Welcome to MSE. Please read this text about how to ask a good question.
    – José Carlos Santos
    Jul 30 at 9:33










  • Do I need to rephrase my question??
    – Sidra Younas
    Jul 30 at 9:35










  • I think that it would be in your best interest to add more details.
    – José Carlos Santos
    Jul 30 at 9:36










  • Alright then, I have an aligned protein sequence file and I need to generate "WAG" matrix from it. The thing is that I have been studying literature regarding wag matrix but I could not get how does it perform calculation??? Does it have a specific formula?? (For example, 'p-distance' is a formula used bu distance matrix) I want to give aligned protein sequence file as input and have a matrix generated as output.
    – Sidra Younas
    Jul 30 at 9:40











  • What I meant was that perhaps that you could edit your question.
    – José Carlos Santos
    Jul 30 at 9:41












up vote
0
down vote

favorite









up vote
0
down vote

favorite











I am working with certain programs in python3.4 (OS is windows). I want to use WAG matrix for phylogeny inference, but I am confused about the formula implemented by it.



For example, in phylogenetics study, when a sequence file is used to generate a distance based matrix, there is a formula called "p-distance" implemented and on the basis of this formula and some standard values for sequence data, a matrix is generated which is later used to construct a tree. When a character based method for tree construction is used, "WAG" is one of the matrices used for likelihood tree construction. What I want to say is that if one wants to implement this matrix, then what is the formula basis for it?




I have an aligned protein sequence file and I need to generate "WAG"
matrix from it. The thing is that I have been studying literature
regarding wag matrix but I could not get how does it perform
calculation??? Does it have a specific formula?? (For example,
'p-distance' is a formula used bu distance matrix) I want to give
aligned protein sequence file as input and have a matrix generated as
output.





matrices python




share|cite|improve this question













I am working with certain programs in python3.4 (OS is windows). I want to use WAG matrix for phylogeny inference, but I am confused about the formula implemented by it.



For example, in phylogenetics study, when a sequence file is used to generate a distance based matrix, there is a formula called "p-distance" implemented and on the basis of this formula and some standard values for sequence data, a matrix is generated which is later used to construct a tree. When a character based method for tree construction is used, "WAG" is one of the matrices used for likelihood tree construction. What I want to say is that if one wants to implement this matrix, then what is the formula basis for it?




I have an aligned protein sequence file and I need to generate "WAG"
matrix from it. The thing is that I have been studying literature
regarding wag matrix but I could not get how does it perform
calculation??? Does it have a specific formula?? (For example,
'p-distance' is a formula used bu distance matrix) I want to give
aligned protein sequence file as input and have a matrix generated as
output.






matrices python





share|cite|improve this question












share|cite|improve this question




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edited Jul 30 at 9:42
























asked Jul 30 at 9:28









Sidra Younas

13




13











  • Welcome to MSE. Please read this text about how to ask a good question.
    – José Carlos Santos
    Jul 30 at 9:33










  • Do I need to rephrase my question??
    – Sidra Younas
    Jul 30 at 9:35










  • I think that it would be in your best interest to add more details.
    – José Carlos Santos
    Jul 30 at 9:36










  • Alright then, I have an aligned protein sequence file and I need to generate "WAG" matrix from it. The thing is that I have been studying literature regarding wag matrix but I could not get how does it perform calculation??? Does it have a specific formula?? (For example, 'p-distance' is a formula used bu distance matrix) I want to give aligned protein sequence file as input and have a matrix generated as output.
    – Sidra Younas
    Jul 30 at 9:40











  • What I meant was that perhaps that you could edit your question.
    – José Carlos Santos
    Jul 30 at 9:41
















  • Welcome to MSE. Please read this text about how to ask a good question.
    – José Carlos Santos
    Jul 30 at 9:33










  • Do I need to rephrase my question??
    – Sidra Younas
    Jul 30 at 9:35










  • I think that it would be in your best interest to add more details.
    – José Carlos Santos
    Jul 30 at 9:36










  • Alright then, I have an aligned protein sequence file and I need to generate "WAG" matrix from it. The thing is that I have been studying literature regarding wag matrix but I could not get how does it perform calculation??? Does it have a specific formula?? (For example, 'p-distance' is a formula used bu distance matrix) I want to give aligned protein sequence file as input and have a matrix generated as output.
    – Sidra Younas
    Jul 30 at 9:40











  • What I meant was that perhaps that you could edit your question.
    – José Carlos Santos
    Jul 30 at 9:41















Welcome to MSE. Please read this text about how to ask a good question.
– José Carlos Santos
Jul 30 at 9:33




Welcome to MSE. Please read this text about how to ask a good question.
– José Carlos Santos
Jul 30 at 9:33












Do I need to rephrase my question??
– Sidra Younas
Jul 30 at 9:35




Do I need to rephrase my question??
– Sidra Younas
Jul 30 at 9:35












I think that it would be in your best interest to add more details.
– José Carlos Santos
Jul 30 at 9:36




I think that it would be in your best interest to add more details.
– José Carlos Santos
Jul 30 at 9:36












Alright then, I have an aligned protein sequence file and I need to generate "WAG" matrix from it. The thing is that I have been studying literature regarding wag matrix but I could not get how does it perform calculation??? Does it have a specific formula?? (For example, 'p-distance' is a formula used bu distance matrix) I want to give aligned protein sequence file as input and have a matrix generated as output.
– Sidra Younas
Jul 30 at 9:40





Alright then, I have an aligned protein sequence file and I need to generate "WAG" matrix from it. The thing is that I have been studying literature regarding wag matrix but I could not get how does it perform calculation??? Does it have a specific formula?? (For example, 'p-distance' is a formula used bu distance matrix) I want to give aligned protein sequence file as input and have a matrix generated as output.
– Sidra Younas
Jul 30 at 9:40













What I meant was that perhaps that you could edit your question.
– José Carlos Santos
Jul 30 at 9:41




What I meant was that perhaps that you could edit your question.
– José Carlos Santos
Jul 30 at 9:41















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