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"Tests for alignment-wide evidence of selection" also confirmed that dachs, merlin, hippo, mats, and warts are the most conserved.

We used the "Tests for alignment-wide evidence of selection" in the Datamonkey webserver to cross-check the data and obtained the same results.

We also used "Tests for alignment-wide evidence of selection" in the Datamonkey webserver (http://www.datamonkey.org) to cross-check the results.

Control samples were analysed with each series of routine samples, results plotted in the software and tested for alignment.

2. Probes without exact matches are then tested for alignment with single base pair mismatches, again using a hash table approach with an expanded dictionary to include all possible mismatch sequences.

Further, the short k-mer length causes Trinity to run considerably more slowly than Oases run with 67-mer, since more words of size k per read have to be constructed and tested for alignment.

Subsequent alignment was undertaken using MUSCLE v 3.8.31 (Edgar 2004) and MK tests for each alignment were conducted using the R package (R Core Team 2011) Popgenome (Pfeifer et al. 2014).

Test data for alignment: We use the following three datasets to test the alignment accuracy of our method.

Similarly, each pred-CA sequence was considered has having no representative in the tested dataset for alignment spanning less than 100nt or having less than 98% identity.

The test data for alignment extension were simulated using phylogenetic trees based on the Ensembl/UCSC tree (http://tinyurl.com/ensembltree; Fig. 3a).

As reported in table 2, only for ALB both null models were rejected in favor of the positive selection models (after Bonferroni correction for two tests, to account for alignment splitting).

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