ISSN:
1432-1432
Keywords:
Evolutionary tree
;
Amino acid sequence
;
Insertion/deletion
;
Bootstrap probability
;
psbA
;
Prochlorothrix
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
Notes:
Summary A maximum likelihood method for inferring protein phylogeny was developed. It is based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages. Therefore, this method is expected to be powerful in inferring phylogeny among distantly related proteins, either orthologous or parallogous, where the evolutionary rate may deviate from constancy. Not only amino acid substitutions but also insertion/deletion events during evolution were incorporated into the Markov model. A simple method for estimating a bootstrap probability for the maximum likelihood tree among alternatives without performing a maximum likelihood estimation for each resampled data set was developed. These methods were applied to amino acid sequence data of a photosynthetic membrane protein,psbA, from photosystem II, and the phylogeny of this protein was discussed in relation to the origin of chloroplasts.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/BF02109483
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