Consensus sequences were then aligned using MUSCLE alignment tool with default parameters in GENEIOUS PRO.
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).
Consensus sequences were compared against the NCBI GenBank database to confirm species identity [ 58] and aligned using the MUSCLE alignment algorithm [ 59].
Inspection of the alignment and comparisons to similar alignments produced using CLUSTALW [ 16] showed that the MUSCLE alignment was better at correctly aligning the zinc coordinating amino acids and fewer manual adjustments were required than with CLUSTALW results (data not shown).
We aligned protein-coding exons in frame, using the amino acid translations as a guide, with the MUSCLE translation alignment plugin [ 75], and we aligned non-coding sequences using the standard MUSCLE alignment plugin in Geneious.
Using the MUSCLE alignment program [ 6], we accurately align query protein domain instances to template domain instances using a stringent threshold length difference ≤ 20% and sequence similarity ≥ 50%) and transfer the possible interactions between template structural domain instances to our query domain instances.
Sequences of GSL1 and GSL2 coding regions were analysed and aligned with their reference sequences by MUSCLE alignment method [ 47] using Geneious software [ 38].
Putative filozoan KLF/SP and nonfilozoan amorphean KLF-DBD amino acid sequences were aligned using default settings of the MUSCLE alignment package in CLCBio (Edgar 2004).
After preprocessing, the unique sequences were aligned in SeaView [ 109], using the muscle alignment option and subsequent manual inspection for each intron separately.
We selected only COSII loci that were identified in two or more of our species, and aligned those sequences in MEGA5 using the MUSCLE alignment tool to assess the proportion of variable sites (Edgar, 2004; Tamura et al., 2011).
The deduced amino acid sequences of the CCD proteins were aligned by a multiple sequence comparison using the log-expectation (MUSCLE) alignment tool (http://www.ebi.ac.uk/Tools/msa/muscle) with the default parameters [ 19].
