recodeMSA: Cmatrix calculation (for developers)
In FranzKrah/rGUIDANCE: rGUIDANCE – alignment confidence score computation in R
recodeMSA R Documentation
Cmatrix calculation (for developers)
Description
Meant for developers only.
Usage
recodeMSA(msa)
Arguments
msa
A MSA of class DNAbin or AAbin
Details
Here implemented as in GUIDANCE program msa_set_score. Characters are represented by odd numbers
and gaps by even numbers.
For more info about the Cmatrix recoding see page 3 on the supplemantary material of: Satija et al. (2009)
http://www.biomedcentral.com/content/supplementary/1471-2148-9-217-s1.pdf
For an example see addMSA
Value
a list with integers
Author(s)
Franz-Sebastian Krah
References
Satija R, Novak A., Mikls I., Lyngs R., and Hein J. (2009) BigFoot:
Bayesian alignment and phylogenetic footprinting with MCMC,
BMC Evolutionary Biology 9:217
Penn et al. 2010. An
alignment confidence score capturing robustness to guide tree uncertainty.
Molecular Biology and Evolution 27:1759–1767.
FranzKrah/rGUIDANCE documentation built on Jan. 27, 2024, 10:42 a.m.
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| recodeMSA | R Documentation |
Cmatrix calculation (for developers)
Description
Meant for developers only.
Usage
recodeMSA(msa)
Arguments
msa |
A MSA of class |
Details
Here implemented as in GUIDANCE program msa_set_score. Characters are represented by odd numbers and gaps by even numbers. For more info about the Cmatrix recoding see page 3 on the supplemantary material of: Satija et al. (2009) http://www.biomedcentral.com/content/supplementary/1471-2148-9-217-s1.pdf
For an example see addMSA
Value
a list with integers
Author(s)
Franz-Sebastian Krah
References
Satija R, Novak A., Mikls I., Lyngs R., and Hein J. (2009) BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC, BMC Evolutionary Biology 9:217
Penn et al. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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