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Hence a systematic, extensive identification and evolution analysis are needed to determine the clear distribution of the genes and to trace their evolutionary histories.
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The methodology of this paper is directly applicable to all decoding algorithms for which a density evolution analysis is possible.
To reconstruct the expansion history of the 16 OsOPT genes in the rice genome, duplication and evolution analysis was performed.
Comparative intron evolution analysis was conducted among 4nAT and other fish species in this study to assess the rate of intron evolution in 4nAT.
Gene family evolution analysis was performed on families that contained ≥2 genes in at least one species and were present in ≥2 species.
The positive selection of the two gene family members were also checked using Likelihood ratio tests (LRTs) with PAML (version 4) [ 82] Gene-expression evolution analysis was done according to [ 55].
When a minimum evolution analysis was performed on the concatenated sequences of the 2 strains and compared with Australian and Thai strains on the MLST website (http://bpseudomallei.mlst.net/), the New Caledonian strains clustered well within groups of Australian sequence types.
The neutrality plot or neutral evolution analysis was performed to determine and compare the extent of influence of mutation pressure and natural selection on the codon usage patterns of MARV by plotting the P12 (GC1,2S) values of the synonymous codons against the P3 (GC3S) values.
The statistical parameters of the co-evolution analysis are in Additional file 9.
Co-evolution analysis is applied to these proteins to identify the correlation between mutated amino acids and functional sites.
To investigate gene duplications and losses during the evolution, reconciliation analysis was performed by using Notung 2.6 [ 32].
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