BLAST pairwise alignments and tree view were generated by using the fast minimum evolution method and maximum sequence difference of 0.75.
For genes with more than one zebra finch ortholog on Ensembl, the pair with least sequence difference (minimum dN + dS) was selected.
The dendrogram were constructed with the following parameters; method-fast minimum evolution, max sequence difference-0.85, distance- grishin (protein).
Tables 4 and 5 show the minimum sequence lengths and run time required for two different accuracy values, given by the aforementioned "Norm 2" that measures the average difference of all the entries in two matrices.
The process of weight calculation based on correlation degree is as follows: First calculate the sequence difference at each moment (Delta_{0i} left( k right)), the maximum and minimum difference (Delta_{max}), (Delta_{min}) according to Eq. 4.
(D.5) is the minimum sequence among sequences in and having the first symbol one at position.
We defined a number of criteria to identify orthologous sequences including minimum alignment length (200 bp), minimum sequence identity (90%), and minimum alignment proportion (> 80% of shorter sequence).
The options employed for SeqMan II assembly were match size = 12 bases, minimum match % = 80, minimum sequence length = 100, maximum added gaps per kb in contig = 70, maximum added gaps per kb in sequence = 70, maximum register shift difference (maximum base pair separation) between matches = 70, gap penalty = 0, and gap length penalty = 0.7.
Alignments with a minimum score identity of 90% and a minimum sequence coverage of 80% were filtered out.
The clusters were created using stringent parameters (minimum overlap length of 40 bp and 95% minimum sequence identity).
