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The final sequence alignment for phylogenetic analysis contained a total of 6998 aligned positions.

These high-quality SNPs were extracted and converted into PHYLIP format multiple sequence alignment for phylogenetic analysis with RAXML v8.2.848 under a GTRGAMMA model (-m GTRGAMMA).

Sequence alignments used for phylogenetic analysis and for the generation of consensus sequences are available online as additional files.

The deduced amino acid sequence was used for sequence alignment and phylogenetic analysis.

Inferred amino acid sequences for each data set were aligned using MUSCLE [ 95] and the coding DNA sequences were then forced onto this alignment for phylogenetic analysis.

Data from a Clustal W alignment [ 30] of nucleocapsid (N) protein sequences were used as input for phylogenetic analysis using MEGA version 4.0 software [ 29].

The final alignment used for phylogenetic analysis consisted of 64 sequences and 16,414 nucleotide positions, of which 473 were variable and 292 were parsimony-informative within horses.

The edited and trimmed multiple sequence alignments were used as the input for phylogenetic analysis.

Sequence alignment and parameters for phylogenetic analysis are provided in Supplemental File S4 which is an executable Nexus file.

We have examined the evolution of eRF1 and eRF3 families using sequence similarity searching, multiple sequence alignment and phylogenetic analysis.

Multiple alignments for phylogenetic analysis were constructed using the MUSCLE program [ 98]; columns containing gaps in >30% of the sequences were discarded.