In 108 (50%) of those cases, the clone matched (i.e. shared a length in common with) that cluster.
The first measure was Faith's Index [1], which reports the shared branch lengths between species in an assemblage as a proportion of the total branch lengths in the species pool phylogeny.
Harris, K. & Nielsen, R. Inferring demographic history from a spectrum of shared haplotype lengths.
Pairwise shared branch-lengths were then used to calculate a variance-covariance matrix, which can be used in mixed multifactor meta-analyses.
This resulted in 10 and five shared full-length ortholog OBPs and CSPs, respectively.
Comparing to the shared full-length elements, the sample capacity increased 30 folds.
Further, the distribution of shared segment lengths was assumed by Huff et al. to be independently exponentially distributed, in which case the coefficient of variation (CV) of the total length of shared segments on a chromosome would be proportional to 1/√ ns.
Furthermore, it does not rely on phylogenetic trees as it is the case with covariance estimation from joint ML, or in covariance estimation methods that model the covariances as a function of shared branch lengths [ 15, 16].
In our analysis we intentionally only included shared, full-length T. foetus sequences to gain insights as to how the presence of endogenous host proteins could affect strategies for drug target identification of the same parasite species.
We identified LTR retrotransposons through three main steps: (1) Construction of a whole-genome comparative map; (2) identification of specific and shared full-length elements by LTR_INSERT; (3) identification of other homologous copies including truncated ones through similarity search.
