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Phenotypic behavior of a group of organisms can be studied using a range of molecular evolutionary tools that help to determine evolutionary relationships.
The progress in molecular evolutionary tools and theoretical concepts for species recognition has recently led to the detection of a continuously increasing number of cryptic species within individual morphological or biological fungal taxa [9] [13] including Hypocrea/Trichoderma [14] [16].
Studies of such genes my provide great insights into the speciation process, but their analysis requires different molecular evolutionary tools, such as methods for measuring and testing the strength of positive Darwinian selection (Yang et al. 2000; Swanson and Vacquier 2002a).
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The recent emergence of the human-pathogenic Vibrio vulnificus in Israel was investigated by using multilocus genotype data and modern molecular evolutionary analysis tools.
This intriguingly broad variation provides an excellent model for studying biological functionality and morphological evolution using the modern tools of molecular evolutionary biology and comparative genomics [ 3, 4].
New techniques and tools have allowed molecular evolutionary biology to blossom in Canada over the last few decades.
Also sequences with regions of unspliced introns were corrected and aligned using MUSCLE alignment tool implemented in Molecular Evolutionary Genetic Analysis software (MEGA 5.0).
Thus, this methodology, with tracing of the molecular evolution using ancestral mutants, is a powerful tool for the analysis of not only the molecular evolutionary process, but also the structural elements of a protein responsible for its various functions.
Genetic diversity and molecular evolutionary studies of neural genes in humans and non-human primates represent powerful tools for understanding cortical development (Enard & Paabo 2004; Gilbert et al. 2005).
The combinatorial approach of molecular evolutionary engineering (or in vitro selection) has also provided a new design tool for functional peptides.
The following section describes the tools used by our pipeline to estimate the descriptors of the molecular evolutionary properties of the markers.
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